data_3IKI
#
_entry.id 3IKI
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.378
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 3IKI pdb_00003iki 10.2210/pdb3iki/pdb
NDB NA0114 ? ?
RCSB RCSB054525 ? ?
WWPDB D_1000054525 ? ?
#
_pdbx_database_status.status_code REL
_pdbx_database_status.entry_id 3IKI
_pdbx_database_status.recvd_initial_deposition_date 2009-08-05
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.SG_entry ?
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.pdb_format_compatible Y
_pdbx_database_status.status_code_nmr_data ?
_pdbx_database_status.methods_development_category ?
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Sheng, J.' 1
'Hassan, A.E.A.' 2
'Zhang, W.' 3
'Gan, J.' 4
'Huang, Z.' 5
#
_citation.id primary
_citation.title 'Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone.'
_citation.journal_abbrev 'Nucleic Acids Res.'
_citation.journal_volume 40
_citation.page_first 8111
_citation.page_last 8118
_citation.year 2012
_citation.journal_id_ASTM NARHAD
_citation.country UK
_citation.journal_id_ISSN 0305-1048
_citation.journal_id_CSD 0389
_citation.book_publisher ?
_citation.pdbx_database_id_PubMed 22641848
_citation.pdbx_database_id_DOI 10.1093/nar/gks426
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Sheng, J.' 1 ?
primary 'Zhang, W.' 2 ?
primary 'Hassan, A.E.' 3 ?
primary 'Gan, J.' 4 ?
primary 'Soares, A.S.' 5 ?
primary 'Geng, S.' 6 ?
primary 'Ren, Y.' 7 ?
primary 'Huang, Z.' 8 ?
#
_cell.entry_id 3IKI
_cell.length_a 42.882
_cell.length_b 42.882
_cell.length_c 23.687
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
_cell.Z_PDB 8
_cell.pdbx_unique_axis ?
_cell.length_a_esd ?
_cell.length_b_esd ?
_cell.length_c_esd ?
_cell.angle_alpha_esd ?
_cell.angle_beta_esd ?
_cell.angle_gamma_esd ?
#
_symmetry.entry_id 3IKI
_symmetry.space_group_name_H-M 'P 43 21 2'
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 96
_symmetry.space_group_name_Hall ?
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer syn "5'-D(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3'" 2537.642 1 ? ? ? ?
2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ?
3 water nat water 18.015 38 ? ? ? ?
#
_entity_poly.entity_id 1
_entity_poly.type polydeoxyribonucleotide
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer yes
_entity_poly.pdbx_seq_one_letter_code '(DG)(UMS)(DG)(US2)(DA)(DC)(DA)(DC)'
_entity_poly.pdbx_seq_one_letter_code_can GUGUACAC
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_target_identifier ?
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 DG n
1 2 UMS n
1 3 DG n
1 4 US2 n
1 5 DA n
1 6 DC n
1 7 DA n
1 8 DC n
#
_pdbx_entity_src_syn.entity_id 1
_pdbx_entity_src_syn.pdbx_src_id 1
_pdbx_entity_src_syn.pdbx_alt_source_flag sample
_pdbx_entity_src_syn.pdbx_beg_seq_num ?
_pdbx_entity_src_syn.pdbx_end_seq_num ?
_pdbx_entity_src_syn.organism_scientific ?
_pdbx_entity_src_syn.organism_common_name ?
_pdbx_entity_src_syn.ncbi_taxonomy_id ?
_pdbx_entity_src_syn.details 'Synthesized by solid phase synthesis'
#
_struct_ref.id 1
_struct_ref.db_name PDB
_struct_ref.db_code 3IKI
_struct_ref.pdbx_db_accession 3IKI
_struct_ref.entity_id 1
_struct_ref.pdbx_align_begin ?
_struct_ref.pdbx_seq_one_letter_code GUGUACAC
_struct_ref.pdbx_db_isoform ?
#
_struct_ref_seq.align_id 1
_struct_ref_seq.ref_id 1
_struct_ref_seq.pdbx_PDB_id_code 3IKI
_struct_ref_seq.pdbx_strand_id A
_struct_ref_seq.seq_align_beg 1
_struct_ref_seq.pdbx_seq_align_beg_ins_code ?
_struct_ref_seq.seq_align_end 8
_struct_ref_seq.pdbx_seq_align_end_ins_code ?
_struct_ref_seq.pdbx_db_accession 3IKI
_struct_ref_seq.db_align_beg 1
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 8
_struct_ref_seq.pdbx_db_align_end_ins_code ?
_struct_ref_seq.pdbx_auth_seq_align_beg 1
_struct_ref_seq.pdbx_auth_seq_align_end 8
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ?
'C10 H14 N5 O6 P' 331.222
DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ?
'C9 H14 N3 O7 P' 307.197
DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ?
'C10 H14 N5 O7 P' 347.221
HOH non-polymer . WATER ? 'H2 O' 18.015
MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305
UMS 'DNA linking' n "2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE" ?
'C10 H15 N2 O8 P Se' 401.168
US2 'DNA linking' n
;2'-deoxy-5-(methylsulfanyl)uridine 5'-(dihydrogen phosphate)
;
"5-SMe-deoxyuridine-5'-phosphate" 'C10 H15 N2 O8 P S' 354.273
#
_exptl.entry_id 3IKI
_exptl.method 'X-RAY DIFFRACTION'
_exptl.crystals_number 1
#
_exptl_crystal.id 1
_exptl_crystal.density_meas ?
_exptl_crystal.density_Matthews 2.15
_exptl_crystal.density_percent_sol 42.67
_exptl_crystal.description ?
_exptl_crystal.F_000 ?
_exptl_crystal.preparation ?
#
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP'
_exptl_crystal_grow.temp 293
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.pH 7.0
_exptl_crystal_grow.pdbx_details
;10% v / v MPD, 40 mM Na Cacodylate pH 7.0, 12 mM Spermine tetra-HCl, 40 mM Lithium Chloride, 80 mM Strontium Chloride /
20 mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
;
_exptl_crystal_grow.pdbx_pH_range ?
#
_diffrn.id 1
_diffrn.ambient_temp 99
_diffrn.ambient_temp_details ?
_diffrn.crystal_id 1
#
_diffrn_detector.diffrn_id 1
_diffrn_detector.detector CCD
_diffrn_detector.type 'ADSC QUANTUM 4'
_diffrn_detector.pdbx_collection_date 2008-10-22
_diffrn_detector.details ?
#
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.monochromator 'channel-cut Si(111) monochromator'
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_scattering_type x-ray
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 0.9795
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.diffrn_id 1
_diffrn_source.source SYNCHROTRON
_diffrn_source.type 'NSLS BEAMLINE X12B'
_diffrn_source.pdbx_synchrotron_site NSLS
_diffrn_source.pdbx_synchrotron_beamline X12B
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_wavelength_list 0.9795
#
_reflns.entry_id 3IKI
_reflns.observed_criterion_sigma_I ?
_reflns.observed_criterion_sigma_F ?
_reflns.d_resolution_low 50
_reflns.d_resolution_high 1.38
_reflns.number_obs 4616
_reflns.number_all 4911
_reflns.percent_possible_obs 94
_reflns.pdbx_Rmerge_I_obs 0.057
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_sigmaI 23.02
_reflns.B_iso_Wilson_estimate ?
_reflns.pdbx_redundancy 8.4
_reflns.R_free_details ?
_reflns.limit_h_max ?
_reflns.limit_h_min ?
_reflns.limit_k_max ?
_reflns.limit_k_min ?
_reflns.limit_l_max ?
_reflns.limit_l_min ?
_reflns.observed_criterion_F_max ?
_reflns.observed_criterion_F_min ?
_reflns.pdbx_chi_squared ?
_reflns.pdbx_scaling_rejects ?
_reflns.pdbx_ordinal 1
_reflns.pdbx_diffrn_id 1
#
_reflns_shell.d_res_high 1.38
_reflns_shell.d_res_low 1.43
_reflns_shell.percent_possible_all 67.8
_reflns_shell.Rmerge_I_obs 0.245
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.meanI_over_sigI_obs 5.86
_reflns_shell.pdbx_redundancy 5.2
_reflns_shell.percent_possible_obs ?
_reflns_shell.number_unique_all 324
_reflns_shell.number_measured_all ?
_reflns_shell.number_measured_obs ?
_reflns_shell.number_unique_obs ?
_reflns_shell.pdbx_chi_squared ?
_reflns_shell.pdbx_ordinal 1
_reflns_shell.pdbx_diffrn_id 1
#
_refine.entry_id 3IKI
_refine.ls_number_reflns_obs 4373
_refine.ls_number_reflns_all 4650
_refine.pdbx_ls_sigma_I ?
_refine.pdbx_ls_sigma_F ?
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.ls_d_res_low 30.32
_refine.ls_d_res_high 1.38
_refine.ls_percent_reflns_obs 94.04
_refine.ls_R_factor_obs ?
_refine.ls_R_factor_all 0.17907
_refine.ls_R_factor_R_work 0.17838
_refine.ls_R_factor_R_free 0.19414
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_percent_reflns_R_free 4.7
_refine.ls_number_reflns_R_free 216
_refine.ls_number_parameters ?
_refine.ls_number_restraints ?
_refine.occupancy_min ?
_refine.occupancy_max ?
_refine.correlation_coeff_Fo_to_Fc 0.957
_refine.correlation_coeff_Fo_to_Fc_free 0.961
_refine.B_iso_mean 12.133
_refine.aniso_B[1][1] 0.12
_refine.aniso_B[2][2] 0.12
_refine.aniso_B[3][3] -0.24
_refine.aniso_B[1][2] 0.00
_refine.aniso_B[1][3] 0.00
_refine.aniso_B[2][3] 0.00
_refine.solvent_model_details MASK
_refine.solvent_model_param_ksol ?
_refine.solvent_model_param_bsol ?
_refine.pdbx_solvent_vdw_probe_radii 1.20
_refine.pdbx_solvent_ion_probe_radii 0.80
_refine.pdbx_solvent_shrinkage_radii 0.80
_refine.pdbx_ls_cross_valid_method THROUGHOUT
_refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS'
_refine.pdbx_starting_model 1DNS
_refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT'
_refine.pdbx_isotropic_thermal_model ?
_refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD'
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_R_Free_selection_details RANDOM
_refine.pdbx_overall_ESU_R 0.061
_refine.pdbx_overall_ESU_R_Free 0.060
_refine.overall_SU_ML 0.031
_refine.overall_SU_B 1.592
_refine.ls_redundancy_reflns_obs ?
_refine.B_iso_min ?
_refine.B_iso_max ?
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.overall_SU_R_free ?
_refine.ls_wR_factor_R_free ?
_refine.ls_wR_factor_R_work ?
_refine.overall_FOM_free_R_set ?
_refine.overall_FOM_work_R_set ?
_refine.pdbx_overall_phase_error ?
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL'
_refine.pdbx_diffrn_id 1
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_Blow_DPI ?
_refine.pdbx_overall_SU_R_free_Blow_DPI ?
#
_refine_analyze.entry_id 3IKI
_refine_analyze.Luzzati_coordinate_error_obs 0.061
_refine_analyze.Luzzati_sigma_a_obs ?
_refine_analyze.Luzzati_d_res_low_obs ?
_refine_analyze.Luzzati_coordinate_error_free 0.060
_refine_analyze.Luzzati_sigma_a_free ?
_refine_analyze.Luzzati_d_res_low_free ?
_refine_analyze.number_disordered_residues ?
_refine_analyze.occupancy_sum_hydrogen ?
_refine_analyze.occupancy_sum_non_hydrogen ?
_refine_analyze.pdbx_Luzzati_d_res_high_obs ?
_refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION'
#
_refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine_hist.cycle_id LAST
_refine_hist.pdbx_number_atoms_protein 0
_refine_hist.pdbx_number_atoms_nucleic_acid 163
_refine_hist.pdbx_number_atoms_ligand 1
_refine_hist.number_atoms_solvent 38
_refine_hist.number_atoms_total 202
_refine_hist.d_res_high 1.38
_refine_hist.d_res_low 30.32
#
loop_
_refine_ls_restr.type
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.weight
_refine_ls_restr.number
_refine_ls_restr.pdbx_refine_id
_refine_ls_restr.pdbx_restraint_function
r_bond_refined_d 0.007 0.021 ? 180 'X-RAY DIFFRACTION' ?
r_angle_refined_deg 1.467 3.000 ? 270 'X-RAY DIFFRACTION' ?
r_chiral_restr 0.057 0.200 ? 31 'X-RAY DIFFRACTION' ?
r_gen_planes_refined 0.007 0.020 ? 83 'X-RAY DIFFRACTION' ?
r_nbd_refined 0.371 0.200 ? 66 'X-RAY DIFFRACTION' ?
r_nbtor_refined 0.277 0.200 ? 103 'X-RAY DIFFRACTION' ?
r_xyhbond_nbd_refined 0.102 0.200 ? 29 'X-RAY DIFFRACTION' ?
r_symmetry_vdw_refined 0.180 0.200 ? 26 'X-RAY DIFFRACTION' ?
r_symmetry_hbond_refined 0.083 0.200 ? 10 'X-RAY DIFFRACTION' ?
r_scbond_it 0.825 3.000 ? 261 'X-RAY DIFFRACTION' ?
r_scangle_it 1.249 4.500 ? 270 'X-RAY DIFFRACTION' ?
#
_refine_ls_shell.pdbx_total_number_of_bins_used 20
_refine_ls_shell.d_res_high 1.380
_refine_ls_shell.d_res_low 1.416
_refine_ls_shell.number_reflns_R_work 216
_refine_ls_shell.R_factor_R_work 0.203
_refine_ls_shell.percent_reflns_obs 65.53
_refine_ls_shell.R_factor_R_free 0.157
_refine_ls_shell.R_factor_R_free_error ?
_refine_ls_shell.percent_reflns_R_free ?
_refine_ls_shell.number_reflns_R_free 14
_refine_ls_shell.number_reflns_all ?
_refine_ls_shell.R_factor_all ?
_refine_ls_shell.number_reflns_obs ?
_refine_ls_shell.redundancy_reflns_obs ?
_refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION'
#
_struct.entry_id 3IKI
_struct.title '5-SMe-dU containing DNA octamer'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 3IKI
_struct_keywords.pdbx_keywords DNA
_struct_keywords.text
;Selenium, Nucleic Acid, 5-SMe-deoxyuridine, 2'-SeMe-deoxyuridine, DNA
;
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 2 ?
C N N 3 ?
#
_struct_biol.id 1
_struct_biol.details ?
#
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
_struct_conn.pdbx_role
covale1 covale both ? A DG 1 "O3'" ? ? ? 1_555 A UMS 2 P ? ? A DG 1 A UMS 2 1_555 ? ? ? ? ? ? ? 1.601 ? ?
covale2 covale both ? A UMS 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A UMS 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.599 ? ?
covale3 covale both ? A DG 3 "O3'" ? ? ? 1_555 A US2 4 P ? ? A DG 3 A US2 4 1_555 ? ? ? ? ? ? ? 1.596 ? ?
covale4 covale both ? A US2 4 "O3'" ? ? ? 1_555 A DA 5 P ? ? A US2 4 A DA 5 1_555 ? ? ? ? ? ? ? 1.597 ? ?
metalc1 metalc ? ? A DG 3 OP2 ? ? ? 1_555 B MG . MG ? ? A DG 3 A MG 11 1_555 ? ? ? ? ? ? ? 2.123 ? ?
metalc2 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 11 A HOH 36 1_555 ? ? ? ? ? ? ? 2.612 ? ?
metalc3 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 11 A HOH 45 1_555 ? ? ? ? ? ? ? 2.680 ? ?
hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 1 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 1 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 1 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog4 hydrog ? ? A UMS 2 N3 ? ? ? 1_555 A DA 7 N1 ? ? A UMS 2 A DA 7 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog5 hydrog ? ? A UMS 2 O4 ? ? ? 1_555 A DA 7 N6 ? ? A UMS 2 A DA 7 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 6 N3 ? ? A DG 3 A DC 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 6 O2 ? ? A DG 3 A DC 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 6 N4 ? ? A DG 3 A DC 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog9 hydrog ? ? A DC 6 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog10 hydrog ? ? A DC 6 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog11 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog12 hydrog ? ? A DA 7 N1 ? ? ? 1_555 A UMS 2 N3 ? ? A DA 7 A UMS 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog13 hydrog ? ? A DA 7 N6 ? ? ? 1_555 A UMS 2 O4 ? ? A DA 7 A UMS 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 8 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 8 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 1 N2 ? ? A DC 8 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
#
loop_
_struct_conn_type.id
_struct_conn_type.criteria
_struct_conn_type.reference
covale ? ?
metalc ? ?
hydrog ? ?
#
_struct_site.id AC1
_struct_site.pdbx_evidence_code Software
_struct_site.pdbx_auth_asym_id A
_struct_site.pdbx_auth_comp_id MG
_struct_site.pdbx_auth_seq_id 11
_struct_site.pdbx_auth_ins_code ?
_struct_site.pdbx_num_residues 4
_struct_site.details 'BINDING SITE FOR RESIDUE MG A 11'
#
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.pdbx_num_res
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.pdbx_auth_ins_code
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_atom_id
_struct_site_gen.label_alt_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 AC1 4 UMS A 2 ? UMS A 2 . ? 1_555 ?
2 AC1 4 DG A 3 ? DG A 3 . ? 1_555 ?
3 AC1 4 HOH C . ? HOH A 36 . ? 1_555 ?
4 AC1 4 HOH C . ? HOH A 45 . ? 1_555 ?
#
_database_PDB_matrix.entry_id 3IKI
_database_PDB_matrix.origx[1][1] 1.000000
_database_PDB_matrix.origx[1][2] 0.000000
_database_PDB_matrix.origx[1][3] 0.000000
_database_PDB_matrix.origx[2][1] 0.000000
_database_PDB_matrix.origx[2][2] 1.000000
_database_PDB_matrix.origx[2][3] 0.000000
_database_PDB_matrix.origx[3][1] 0.000000
_database_PDB_matrix.origx[3][2] 0.000000
_database_PDB_matrix.origx[3][3] 1.000000
_database_PDB_matrix.origx_vector[1] 0.00000
_database_PDB_matrix.origx_vector[2] 0.00000
_database_PDB_matrix.origx_vector[3] 0.00000
#
_atom_sites.entry_id 3IKI
_atom_sites.fract_transf_matrix[1][1] 0.023320
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.000000
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.023320
_atom_sites.fract_transf_matrix[2][3] 0.000000
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] 0.000000
_atom_sites.fract_transf_matrix[3][3] 0.042217
_atom_sites.fract_transf_vector[1] 0.00000
_atom_sites.fract_transf_vector[2] 0.00000
_atom_sites.fract_transf_vector[3] 0.00000
#
loop_
_atom_type.symbol
C
MG
N
O
P
S
SE
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 1 O "O5'" . DG A 1 1 ? 29.200 19.006 -5.269 1.00 10.16 ? 1 DG A "O5'" 1
ATOM 2 C "C5'" . DG A 1 1 ? 29.102 17.599 -5.012 1.00 8.50 ? 1 DG A "C5'" 1
ATOM 3 C "C4'" . DG A 1 1 ? 30.337 17.073 -4.294 1.00 8.52 ? 1 DG A "C4'" 1
ATOM 4 O "O4'" . DG A 1 1 ? 31.516 17.253 -5.121 1.00 8.26 ? 1 DG A "O4'" 1
ATOM 5 C "C3'" . DG A 1 1 ? 30.689 17.780 -2.994 1.00 8.15 ? 1 DG A "C3'" 1
ATOM 6 O "O3'" . DG A 1 1 ? 29.917 17.237 -1.924 1.00 8.52 ? 1 DG A "O3'" 1
ATOM 7 C "C2'" . DG A 1 1 ? 32.172 17.447 -2.873 1.00 8.35 ? 1 DG A "C2'" 1
ATOM 8 C "C1'" . DG A 1 1 ? 32.630 17.593 -4.320 1.00 8.79 ? 1 DG A "C1'" 1
ATOM 9 N N9 . DG A 1 1 ? 33.046 18.962 -4.621 1.00 8.63 ? 1 DG A N9 1
ATOM 10 C C8 . DG A 1 1 ? 32.299 19.947 -5.227 1.00 9.29 ? 1 DG A C8 1
ATOM 11 N N7 . DG A 1 1 ? 32.930 21.082 -5.340 1.00 9.41 ? 1 DG A N7 1
ATOM 12 C C5 . DG A 1 1 ? 34.171 20.842 -4.765 1.00 8.80 ? 1 DG A C5 1
ATOM 13 C C6 . DG A 1 1 ? 35.285 21.702 -4.603 1.00 8.54 ? 1 DG A C6 1
ATOM 14 O O6 . DG A 1 1 ? 35.392 22.885 -4.953 1.00 9.84 ? 1 DG A O6 1
ATOM 15 N N1 . DG A 1 1 ? 36.351 21.070 -3.970 1.00 9.08 ? 1 DG A N1 1
ATOM 16 C C2 . DG A 1 1 ? 36.342 19.757 -3.553 1.00 9.48 ? 1 DG A C2 1
ATOM 17 N N2 . DG A 1 1 ? 37.462 19.309 -2.967 1.00 10.47 ? 1 DG A N2 1
ATOM 18 N N3 . DG A 1 1 ? 35.307 18.934 -3.701 1.00 9.12 ? 1 DG A N3 1
ATOM 19 C C4 . DG A 1 1 ? 34.257 19.542 -4.310 1.00 8.79 ? 1 DG A C4 1
HETATM 20 P P . UMS A 1 2 ? 29.421 18.150 -0.706 1.00 9.05 ? 2 UMS A P 1
HETATM 21 O OP1 . UMS A 1 2 ? 28.566 17.307 0.151 1.00 10.34 ? 2 UMS A OP1 1
HETATM 22 O OP2 . UMS A 1 2 ? 28.924 19.445 -1.225 1.00 10.47 ? 2 UMS A OP2 1
HETATM 23 O "O5'" . UMS A 1 2 ? 30.757 18.496 0.103 1.00 8.89 ? 2 UMS A "O5'" 1
HETATM 24 C "C5'" . UMS A 1 2 ? 31.441 17.472 0.807 1.00 8.83 ? 2 UMS A "C5'" 1
HETATM 25 C "C4'" . UMS A 1 2 ? 32.791 17.955 1.276 1.00 9.12 ? 2 UMS A "C4'" 1
HETATM 26 O "O4'" . UMS A 1 2 ? 33.581 18.369 0.134 1.00 8.82 ? 2 UMS A "O4'" 1
HETATM 27 C "C3'" . UMS A 1 2 ? 32.756 19.173 2.179 1.00 10.51 ? 2 UMS A "C3'" 1
HETATM 28 O "O3'" . UMS A 1 2 ? 32.423 18.731 3.481 1.00 12.79 ? 2 UMS A "O3'" 1
HETATM 29 C "C2'" . UMS A 1 2 ? 34.192 19.676 2.028 1.00 9.97 ? 2 UMS A "C2'" 1
HETATM 30 SE "SE2'" . UMS A 1 2 ? 35.473 18.592 3.062 0.80 11.05 ? 2 UMS A "SE2'" 1
HETATM 31 C "C1'" . UMS A 1 2 ? 34.417 19.438 0.533 1.00 8.91 ? 2 UMS A "C1'" 1
HETATM 32 C "CA'" . UMS A 1 2 ? 37.126 19.644 2.969 1.00 11.95 ? 2 UMS A "CA'" 1
HETATM 33 N N1 . UMS A 1 2 ? 34.107 20.625 -0.339 1.00 9.25 ? 2 UMS A N1 1
HETATM 34 C C2 . UMS A 1 2 ? 35.086 21.588 -0.498 1.00 9.47 ? 2 UMS A C2 1
HETATM 35 O O2 . UMS A 1 2 ? 36.173 21.525 0.045 1.00 10.23 ? 2 UMS A O2 1
HETATM 36 N N3 . UMS A 1 2 ? 34.746 22.642 -1.310 1.00 9.45 ? 2 UMS A N3 1
HETATM 37 C C4 . UMS A 1 2 ? 33.543 22.828 -1.974 1.00 9.06 ? 2 UMS A C4 1
HETATM 38 O O4 . UMS A 1 2 ? 33.389 23.829 -2.666 1.00 9.46 ? 2 UMS A O4 1
HETATM 39 C C5 . UMS A 1 2 ? 32.565 21.787 -1.765 1.00 9.55 ? 2 UMS A C5 1
HETATM 40 C C6 . UMS A 1 2 ? 32.877 20.746 -0.974 1.00 9.05 ? 2 UMS A C6 1
ATOM 41 P P . DG A 1 3 ? 31.679 19.652 4.556 1.00 15.71 ? 3 DG A P 1
ATOM 42 O OP1 . DG A 1 3 ? 31.260 18.752 5.651 1.00 17.09 ? 3 DG A OP1 1
ATOM 43 O OP2 . DG A 1 3 ? 30.721 20.539 3.869 1.00 16.48 ? 3 DG A OP2 1
ATOM 44 O "O5'" . DG A 1 3 ? 32.908 20.543 5.059 1.00 15.23 ? 3 DG A "O5'" 1
ATOM 45 C "C5'" . DG A 1 3 ? 32.843 21.945 5.006 1.00 13.73 ? 3 DG A "C5'" 1
ATOM 46 C "C4'" . DG A 1 3 ? 34.257 22.474 4.941 1.00 13.22 ? 3 DG A "C4'" 1
ATOM 47 O "O4'" . DG A 1 3 ? 34.749 22.336 3.591 1.00 12.36 ? 3 DG A "O4'" 1
ATOM 48 C "C3'" . DG A 1 3 ? 34.357 23.950 5.234 1.00 12.39 ? 3 DG A "C3'" 1
ATOM 49 O "O3'" . DG A 1 3 ? 34.459 24.186 6.669 1.00 9.15 ? 3 DG A "O3'" 1
ATOM 50 C "C2'" . DG A 1 3 ? 35.586 24.360 4.437 1.00 11.58 ? 3 DG A "C2'" 1
ATOM 51 C "C1'" . DG A 1 3 ? 35.429 23.505 3.188 1.00 10.43 ? 3 DG A "C1'" 1
ATOM 52 N N9 . DG A 1 3 ? 34.648 24.135 2.126 1.00 10.22 ? 3 DG A N9 1
ATOM 53 C C8 . DG A 1 3 ? 33.428 23.744 1.627 1.00 9.97 ? 3 DG A C8 1
ATOM 54 N N7 . DG A 1 3 ? 32.986 24.510 0.667 1.00 9.92 ? 3 DG A N7 1
ATOM 55 C C5 . DG A 1 3 ? 33.985 25.467 0.517 1.00 9.40 ? 3 DG A C5 1
ATOM 56 C C6 . DG A 1 3 ? 34.076 26.571 -0.367 1.00 8.93 ? 3 DG A C6 1
ATOM 57 O O6 . DG A 1 3 ? 33.263 26.922 -1.229 1.00 9.41 ? 3 DG A O6 1
ATOM 58 N N1 . DG A 1 3 ? 35.255 27.297 -0.184 1.00 9.13 ? 3 DG A N1 1
ATOM 59 C C2 . DG A 1 3 ? 36.230 27.001 0.742 1.00 9.39 ? 3 DG A C2 1
ATOM 60 N N2 . DG A 1 3 ? 37.307 27.803 0.793 1.00 9.27 ? 3 DG A N2 1
ATOM 61 N N3 . DG A 1 3 ? 36.160 25.968 1.570 1.00 9.25 ? 3 DG A N3 1
ATOM 62 C C4 . DG A 1 3 ? 35.013 25.252 1.407 1.00 9.74 ? 3 DG A C4 1
HETATM 63 P P . US2 A 1 4 ? 34.000 25.547 7.366 1.00 9.16 ? 4 US2 A P 1
HETATM 64 N N1 . US2 A 1 4 ? 35.349 29.061 3.421 1.00 5.92 ? 4 US2 A N1 1
HETATM 65 C C6 . US2 A 1 4 ? 34.393 28.074 3.644 1.00 5.69 ? 4 US2 A C6 1
HETATM 66 C C2 . US2 A 1 4 ? 35.177 30.017 2.439 1.00 4.71 ? 4 US2 A C2 1
HETATM 67 O O2 . US2 A 1 4 ? 35.968 30.918 2.207 1.00 4.70 ? 4 US2 A O2 1
HETATM 68 N N3 . US2 A 1 4 ? 34.017 29.894 1.719 1.00 5.07 ? 4 US2 A N3 1
HETATM 69 C C4 . US2 A 1 4 ? 33.024 28.938 1.884 1.00 5.05 ? 4 US2 A C4 1
HETATM 70 O O4 . US2 A 1 4 ? 32.024 28.926 1.172 1.00 5.04 ? 4 US2 A O4 1
HETATM 71 C C5 . US2 A 1 4 ? 33.257 27.957 2.936 1.00 5.87 ? 4 US2 A C5 1
HETATM 72 S S5 . US2 A 1 4 ? 32.100 26.680 3.276 1.00 6.82 ? 4 US2 A S5 1
HETATM 73 C C5A . US2 A 1 4 ? 30.857 27.447 4.289 1.00 9.62 ? 4 US2 A C5A 1
HETATM 74 C "C1'" . US2 A 1 4 ? 36.597 29.111 4.259 1.00 5.73 ? 4 US2 A "C1'" 1
HETATM 75 O "O4'" . US2 A 1 4 ? 36.828 27.841 4.861 1.00 7.43 ? 4 US2 A "O4'" 1
HETATM 76 C "C4'" . US2 A 1 4 ? 36.862 28.001 6.302 1.00 6.32 ? 4 US2 A "C4'" 1
HETATM 77 C "C3'" . US2 A 1 4 ? 36.066 29.277 6.546 1.00 5.74 ? 4 US2 A "C3'" 1
HETATM 78 O "O3'" . US2 A 1 4 ? 36.420 29.819 7.805 1.00 5.91 ? 4 US2 A "O3'" 1
HETATM 79 C "C2'" . US2 A 1 4 ? 36.527 30.143 5.380 1.00 6.02 ? 4 US2 A "C2'" 1
HETATM 80 C "C5'" . US2 A 1 4 ? 36.305 26.760 6.964 1.00 7.21 ? 4 US2 A "C5'" 1
HETATM 81 O "O5'" . US2 A 1 4 ? 34.908 26.665 6.673 1.00 7.56 ? 4 US2 A "O5'" 1
HETATM 82 O O1P . US2 A 1 4 ? 32.584 25.785 7.061 1.00 8.52 ? 4 US2 A O1P 1
HETATM 83 O O2P . US2 A 1 4 ? 34.409 25.429 8.789 1.00 11.42 ? 4 US2 A O2P 1
ATOM 84 P P . DA A 1 5 ? 35.464 30.875 8.528 1.00 6.43 ? 5 DA A P 1
ATOM 85 O OP1 . DA A 1 5 ? 35.871 30.926 9.984 1.00 11.11 ? 5 DA A OP1 1
ATOM 86 O OP2 . DA A 1 5 ? 34.015 30.623 8.221 1.00 11.96 ? 5 DA A OP2 1
ATOM 87 O "O5'" . DA A 1 5 ? 35.911 32.253 7.849 1.00 8.28 ? 5 DA A "O5'" 1
ATOM 88 C "C5'" . DA A 1 5 ? 35.012 33.322 7.615 1.00 8.06 ? 5 DA A "C5'" 1
ATOM 89 C "C4'" . DA A 1 5 ? 35.548 34.164 6.476 1.00 7.41 ? 5 DA A "C4'" 1
ATOM 90 O "O4'" . DA A 1 5 ? 35.696 33.336 5.293 1.00 7.13 ? 5 DA A "O4'" 1
ATOM 91 C "C3'" . DA A 1 5 ? 34.652 35.320 6.061 1.00 7.28 ? 5 DA A "C3'" 1
ATOM 92 O "O3'" . DA A 1 5 ? 34.988 36.456 6.830 1.00 7.95 ? 5 DA A "O3'" 1
ATOM 93 C "C2'" . DA A 1 5 ? 35.028 35.501 4.599 1.00 7.02 ? 5 DA A "C2'" 1
ATOM 94 C "C1'" . DA A 1 5 ? 35.185 34.047 4.179 1.00 6.99 ? 5 DA A "C1'" 1
ATOM 95 N N9 . DA A 1 5 ? 33.962 33.373 3.730 1.00 6.98 ? 5 DA A N9 1
ATOM 96 C C8 . DA A 1 5 ? 33.331 32.310 4.324 1.00 6.83 ? 5 DA A C8 1
ATOM 97 N N7 . DA A 1 5 ? 32.272 31.890 3.684 1.00 6.48 ? 5 DA A N7 1
ATOM 98 C C5 . DA A 1 5 ? 32.207 32.728 2.581 1.00 6.74 ? 5 DA A C5 1
ATOM 99 C C6 . DA A 1 5 ? 31.308 32.799 1.496 1.00 6.78 ? 5 DA A C6 1
ATOM 100 N N6 . DA A 1 5 ? 30.269 31.973 1.356 1.00 7.73 ? 5 DA A N6 1
ATOM 101 N N1 . DA A 1 5 ? 31.527 33.754 0.563 1.00 6.47 ? 5 DA A N1 1
ATOM 102 C C2 . DA A 1 5 ? 32.568 34.588 0.708 1.00 6.79 ? 5 DA A C2 1
ATOM 103 N N3 . DA A 1 5 ? 33.482 34.609 1.683 1.00 7.00 ? 5 DA A N3 1
ATOM 104 C C4 . DA A 1 5 ? 33.243 33.648 2.590 1.00 6.90 ? 5 DA A C4 1
ATOM 105 P P . DC A 1 6 ? 33.841 37.463 7.312 1.00 8.67 ? 6 DC A P 1
ATOM 106 O OP1 . DC A 1 6 ? 34.510 38.533 8.086 1.00 10.25 ? 6 DC A OP1 1
ATOM 107 O OP2 . DC A 1 6 ? 32.725 36.701 7.902 1.00 9.64 ? 6 DC A OP2 1
ATOM 108 O "O5'" . DC A 1 6 ? 33.299 38.098 5.953 1.00 8.66 ? 6 DC A "O5'" 1
ATOM 109 C "C5'" . DC A 1 6 ? 34.115 38.996 5.212 1.00 8.90 ? 6 DC A "C5'" 1
ATOM 110 C "C4'" . DC A 1 6 ? 33.433 39.330 3.903 1.00 8.84 ? 6 DC A "C4'" 1
ATOM 111 O "O4'" . DC A 1 6 ? 33.276 38.127 3.112 1.00 8.37 ? 6 DC A "O4'" 1
ATOM 112 C "C3'" . DC A 1 6 ? 32.008 39.846 4.052 1.00 9.06 ? 6 DC A "C3'" 1
ATOM 113 O "O3'" . DC A 1 6 ? 31.997 41.215 4.436 1.00 11.60 ? 6 DC A "O3'" 1
ATOM 114 C "C2'" . DC A 1 6 ? 31.474 39.623 2.646 1.00 9.16 ? 6 DC A "C2'" 1
ATOM 115 C "C1'" . DC A 1 6 ? 32.063 38.243 2.378 1.00 8.32 ? 6 DC A "C1'" 1
ATOM 116 N N1 . DC A 1 6 ? 31.150 37.101 2.714 1.00 7.75 ? 6 DC A N1 1
ATOM 117 C C2 . DC A 1 6 ? 30.116 36.786 1.819 1.00 7.70 ? 6 DC A C2 1
ATOM 118 O O2 . DC A 1 6 ? 29.989 37.475 0.796 1.00 7.91 ? 6 DC A O2 1
ATOM 119 N N3 . DC A 1 6 ? 29.291 35.742 2.101 1.00 7.18 ? 6 DC A N3 1
ATOM 120 C C4 . DC A 1 6 ? 29.457 35.031 3.220 1.00 7.76 ? 6 DC A C4 1
ATOM 121 N N4 . DC A 1 6 ? 28.618 34.015 3.441 1.00 8.11 ? 6 DC A N4 1
ATOM 122 C C5 . DC A 1 6 ? 30.498 35.334 4.154 1.00 7.58 ? 6 DC A C5 1
ATOM 123 C C6 . DC A 1 6 ? 31.310 36.364 3.862 1.00 7.28 ? 6 DC A C6 1
ATOM 124 P P . DA A 1 7 ? 30.748 41.815 5.233 1.00 12.50 ? 7 DA A P 1
ATOM 125 O OP1 . DA A 1 7 ? 31.143 43.167 5.712 1.00 13.31 ? 7 DA A OP1 1
ATOM 126 O OP2 . DA A 1 7 ? 30.200 40.812 6.184 1.00 12.61 ? 7 DA A OP2 1
ATOM 127 O "O5'" . DA A 1 7 ? 29.674 41.979 4.066 1.00 10.71 ? 7 DA A "O5'" 1
ATOM 128 C "C5'" . DA A 1 7 ? 29.871 42.930 3.021 1.00 10.74 ? 7 DA A "C5'" 1
ATOM 129 C "C4'" . DA A 1 7 ? 28.691 42.841 2.080 1.00 10.31 ? 7 DA A "C4'" 1
ATOM 130 O "O4'" . DA A 1 7 ? 28.595 41.503 1.539 1.00 10.39 ? 7 DA A "O4'" 1
ATOM 131 C "C3'" . DA A 1 7 ? 27.355 43.064 2.759 1.00 10.10 ? 7 DA A "C3'" 1
ATOM 132 O "O3'" . DA A 1 7 ? 27.099 44.453 2.799 1.00 11.17 ? 7 DA A "O3'" 1
ATOM 133 C "C2'" . DA A 1 7 ? 26.372 42.323 1.866 1.00 9.62 ? 7 DA A "C2'" 1
ATOM 134 C "C1'" . DA A 1 7 ? 27.228 41.153 1.415 1.00 8.62 ? 7 DA A "C1'" 1
ATOM 135 N N9 . DA A 1 7 ? 27.059 39.889 2.126 1.00 7.80 ? 7 DA A N9 1
ATOM 136 C C8 . DA A 1 7 ? 27.800 39.405 3.176 1.00 7.82 ? 7 DA A C8 1
ATOM 137 N N7 . DA A 1 7 ? 27.417 38.216 3.582 1.00 7.61 ? 7 DA A N7 1
ATOM 138 C C5 . DA A 1 7 ? 26.367 37.889 2.732 1.00 7.83 ? 7 DA A C5 1
ATOM 139 C C6 . DA A 1 7 ? 25.528 36.753 2.631 1.00 7.91 ? 7 DA A C6 1
ATOM 140 N N6 . DA A 1 7 ? 25.646 35.687 3.429 1.00 7.48 ? 7 DA A N6 1
ATOM 141 N N1 . DA A 1 7 ? 24.565 36.759 1.671 1.00 7.87 ? 7 DA A N1 1
ATOM 142 C C2 . DA A 1 7 ? 24.451 37.829 0.872 1.00 8.14 ? 7 DA A C2 1
ATOM 143 N N3 . DA A 1 7 ? 25.180 38.948 0.868 1.00 8.36 ? 7 DA A N3 1
ATOM 144 C C4 . DA A 1 7 ? 26.129 38.914 1.832 1.00 7.77 ? 7 DA A C4 1
ATOM 145 P P . DC A 1 8 ? 26.210 45.061 3.972 1.00 12.05 ? 8 DC A P 1
ATOM 146 O OP1 . DC A 1 8 ? 26.241 46.534 3.785 1.00 13.06 ? 8 DC A OP1 1
ATOM 147 O OP2 . DC A 1 8 ? 26.633 44.487 5.270 1.00 13.42 ? 8 DC A OP2 1
ATOM 148 O "O5'" . DC A 1 8 ? 24.739 44.550 3.635 1.00 10.98 ? 8 DC A "O5'" 1
ATOM 149 C "C5'" . DC A 1 8 ? 24.082 45.070 2.478 1.00 12.10 ? 8 DC A "C5'" 1
ATOM 150 C "C4'" . DC A 1 8 ? 22.739 44.413 2.247 1.00 12.17 ? 8 DC A "C4'" 1
ATOM 151 O "O4'" . DC A 1 8 ? 22.941 42.978 2.152 1.00 11.58 ? 8 DC A "O4'" 1
ATOM 152 C "C3'" . DC A 1 8 ? 21.697 44.661 3.337 1.00 13.10 ? 8 DC A "C3'" 1
ATOM 153 O "O3'" . DC A 1 8 ? 20.459 45.014 2.731 1.00 15.88 ? 8 DC A "O3'" 1
ATOM 154 C "C2'" . DC A 1 8 ? 21.588 43.326 4.064 1.00 12.36 ? 8 DC A "C2'" 1
ATOM 155 C "C1'" . DC A 1 8 ? 22.026 42.318 3.000 1.00 11.18 ? 8 DC A "C1'" 1
ATOM 156 N N1 . DC A 1 8 ? 22.660 41.111 3.609 1.00 10.63 ? 8 DC A N1 1
ATOM 157 C C2 . DC A 1 8 ? 22.120 39.835 3.369 1.00 10.15 ? 8 DC A C2 1
ATOM 158 O O2 . DC A 1 8 ? 21.129 39.713 2.636 1.00 10.11 ? 8 DC A O2 1
ATOM 159 N N3 . DC A 1 8 ? 22.703 38.758 3.962 1.00 9.75 ? 8 DC A N3 1
ATOM 160 C C4 . DC A 1 8 ? 23.775 38.913 4.752 1.00 9.68 ? 8 DC A C4 1
ATOM 161 N N4 . DC A 1 8 ? 24.308 37.819 5.314 1.00 9.22 ? 8 DC A N4 1
ATOM 162 C C5 . DC A 1 8 ? 24.348 40.201 4.997 1.00 9.76 ? 8 DC A C5 1
ATOM 163 C C6 . DC A 1 8 ? 23.760 41.254 4.418 1.00 10.05 ? 8 DC A C6 1
HETATM 164 MG MG . MG B 2 . ? 30.594 21.925 2.266 1.00 31.29 ? 11 MG A MG 1
HETATM 165 O O . HOH C 3 . ? 26.127 47.810 1.437 1.00 13.71 ? 21 HOH A O 1
HETATM 166 O O . HOH C 3 . ? 26.150 16.493 -0.750 1.00 14.32 ? 22 HOH A O 1
HETATM 167 O O . HOH C 3 . ? 20.901 38.797 -0.009 1.00 14.62 ? 23 HOH A O 1
HETATM 168 O O . HOH C 3 . ? 31.380 25.824 -2.831 1.00 12.64 ? 24 HOH A O 1
HETATM 169 O O . HOH C 3 . ? 30.001 31.134 4.980 1.00 22.12 ? 25 HOH A O 1
HETATM 170 O O . HOH C 3 . ? 30.445 24.463 6.091 1.00 21.24 ? 26 HOH A O 1
HETATM 171 O O . HOH C 3 . ? 28.446 19.637 -7.900 1.00 16.25 ? 27 HOH A O 1
HETATM 172 O O . HOH C 3 . ? 27.354 16.965 -8.501 1.00 13.17 ? 28 HOH A O 1
HETATM 173 O O . HOH C 3 . ? 17.937 38.605 0.026 1.00 20.65 ? 29 HOH A O 1
HETATM 174 O O . HOH C 3 . ? 22.697 39.803 -2.060 1.00 19.48 ? 30 HOH A O 1
HETATM 175 O O . HOH C 3 . ? 38.849 16.919 -2.726 1.00 16.74 ? 31 HOH A O 1
HETATM 176 O O . HOH C 3 . ? 30.500 24.434 -0.487 1.00 20.02 ? 32 HOH A O 1
HETATM 177 O O . HOH C 3 . ? 24.599 15.506 1.395 1.00 23.24 ? 33 HOH A O 1
HETATM 178 O O . HOH C 3 . ? 31.516 34.034 7.443 1.00 17.86 ? 34 HOH A O 1
HETATM 179 O O . HOH C 3 . ? 25.912 42.750 7.039 1.00 21.98 ? 35 HOH A O 1
HETATM 180 O O . HOH C 3 . ? 29.131 21.894 0.102 1.00 21.99 ? 36 HOH A O 1
HETATM 181 O O . HOH C 3 . ? 31.412 22.863 -6.608 1.00 25.02 ? 37 HOH A O 1
HETATM 182 O O . HOH C 3 . ? 28.058 16.946 2.594 1.00 23.32 ? 38 HOH A O 1
HETATM 183 O O . HOH C 3 . ? 36.191 22.681 8.803 1.00 29.16 ? 39 HOH A O 1
HETATM 184 O O . HOH C 3 . ? 31.869 31.924 8.993 1.00 24.12 ? 40 HOH A O 1
HETATM 185 O O . HOH C 3 . ? 33.958 24.660 -6.285 1.00 20.77 ? 41 HOH A O 1
HETATM 186 O O . HOH C 3 . ? 27.858 20.417 -3.417 1.00 25.85 ? 42 HOH A O 1
HETATM 187 O O . HOH C 3 . ? 27.643 40.706 7.127 1.00 23.54 ? 43 HOH A O 1
HETATM 188 O O . HOH C 3 . ? 33.491 35.652 10.465 1.00 21.88 ? 44 HOH A O 1
HETATM 189 O O . HOH C 3 . ? 29.641 24.046 3.599 1.00 23.74 ? 45 HOH A O 1
HETATM 190 O O . HOH C 3 . ? 28.934 33.312 6.511 1.00 32.35 ? 46 HOH A O 1
HETATM 191 O O . HOH C 3 . ? 27.987 36.709 5.986 1.00 22.00 ? 47 HOH A O 1
HETATM 192 O O . HOH C 3 . ? 31.394 15.811 5.287 1.00 20.11 ? 48 HOH A O 1
HETATM 193 O O . HOH C 3 . ? 28.330 29.985 2.990 1.00 26.87 ? 49 HOH A O 1
HETATM 194 O O . HOH C 3 . ? 30.282 37.852 7.579 1.00 28.99 ? 50 HOH A O 1
HETATM 195 O O . HOH C 3 . ? 29.414 28.245 1.159 1.00 25.65 ? 51 HOH A O 1
HETATM 196 O O . HOH C 3 . ? 28.847 15.069 4.238 1.00 25.43 ? 52 HOH A O 1
HETATM 197 O O . HOH C 3 . ? 28.955 45.075 6.394 1.00 30.65 ? 53 HOH A O 1
HETATM 198 O O . HOH C 3 . ? 32.407 28.590 7.481 1.00 30.58 ? 54 HOH A O 1
HETATM 199 O O . HOH C 3 . ? 37.313 21.663 6.220 1.00 33.94 ? 55 HOH A O 1
HETATM 200 O O . HOH C 3 . ? 31.532 25.157 10.542 1.00 40.65 ? 56 HOH A O 1
HETATM 201 O O . HOH C 3 . ? 35.859 36.172 1.345 1.00 8.40 ? 57 HOH A O 1
HETATM 202 O O . HOH C 3 . ? 23.926 41.410 -0.257 1.00 14.40 ? 58 HOH A O 1
#
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
A 1 1 DG 1 1 1 DG G A . n
A 1 2 UMS 2 2 2 UMS UMS A . n
A 1 3 DG 3 3 3 DG G A . n
A 1 4 US2 4 4 4 US2 USM A . n
A 1 5 DA 5 5 5 DA A A . n
A 1 6 DC 6 6 6 DC C A . n
A 1 7 DA 7 7 7 DA A A . n
A 1 8 DC 8 8 8 DC C A . n
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 MG 1 11 11 MG MG A .
C 3 HOH 1 21 21 HOH HOH A .
C 3 HOH 2 22 22 HOH HOH A .
C 3 HOH 3 23 23 HOH HOH A .
C 3 HOH 4 24 24 HOH HOH A .
C 3 HOH 5 25 25 HOH HOH A .
C 3 HOH 6 26 26 HOH HOH A .
C 3 HOH 7 27 27 HOH HOH A .
C 3 HOH 8 28 28 HOH HOH A .
C 3 HOH 9 29 29 HOH HOH A .
C 3 HOH 10 30 30 HOH HOH A .
C 3 HOH 11 31 31 HOH HOH A .
C 3 HOH 12 32 32 HOH HOH A .
C 3 HOH 13 33 33 HOH HOH A .
C 3 HOH 14 34 34 HOH HOH A .
C 3 HOH 15 35 35 HOH HOH A .
C 3 HOH 16 36 36 HOH HOH A .
C 3 HOH 17 37 37 HOH HOH A .
C 3 HOH 18 38 38 HOH HOH A .
C 3 HOH 19 39 39 HOH HOH A .
C 3 HOH 20 40 40 HOH HOH A .
C 3 HOH 21 41 41 HOH HOH A .
C 3 HOH 22 42 42 HOH HOH A .
C 3 HOH 23 43 43 HOH HOH A .
C 3 HOH 24 44 44 HOH HOH A .
C 3 HOH 25 45 45 HOH HOH A .
C 3 HOH 26 46 46 HOH HOH A .
C 3 HOH 27 47 47 HOH HOH A .
C 3 HOH 28 48 48 HOH HOH A .
C 3 HOH 29 49 49 HOH HOH A .
C 3 HOH 30 50 50 HOH HOH A .
C 3 HOH 31 51 51 HOH HOH A .
C 3 HOH 32 52 52 HOH HOH A .
C 3 HOH 33 53 53 HOH HOH A .
C 3 HOH 34 54 54 HOH HOH A .
C 3 HOH 35 55 55 HOH HOH A .
C 3 HOH 36 56 56 HOH HOH A .
C 3 HOH 37 57 57 HOH HOH A .
C 3 HOH 38 58 58 HOH HOH A .
#
loop_
_pdbx_struct_mod_residue.id
_pdbx_struct_mod_residue.label_asym_id
_pdbx_struct_mod_residue.label_comp_id
_pdbx_struct_mod_residue.label_seq_id
_pdbx_struct_mod_residue.auth_asym_id
_pdbx_struct_mod_residue.auth_comp_id
_pdbx_struct_mod_residue.auth_seq_id
_pdbx_struct_mod_residue.PDB_ins_code
_pdbx_struct_mod_residue.parent_comp_id
_pdbx_struct_mod_residue.details
1 A UMS 2 A UMS 2 ? DU ?
2 A US2 4 A US2 4 ? DU ?
#
_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_and_software_defined_assembly
_pdbx_struct_assembly.method_details PISA
_pdbx_struct_assembly.oligomeric_details dimeric
_pdbx_struct_assembly.oligomeric_count 2
#
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1,2
_pdbx_struct_assembly_gen.asym_id_list A,B,C
#
loop_
_pdbx_struct_assembly_prop.biol_id
_pdbx_struct_assembly_prop.type
_pdbx_struct_assembly_prop.value
_pdbx_struct_assembly_prop.details
1 'ABSA (A^2)' 2240 ?
1 MORE -12 ?
1 'SSA (A^2)' 2810 ?
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
2 'crystal symmetry operation' 7_555 y,x,-z 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000
#
loop_
_pdbx_struct_conn_angle.id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_alt_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr1_auth_atom_id
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_PDB_ins_code
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_alt_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_comp_id
_pdbx_struct_conn_angle.ptnr2_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_atom_id
_pdbx_struct_conn_angle.ptnr2_auth_asym_id
_pdbx_struct_conn_angle.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_PDB_ins_code
_pdbx_struct_conn_angle.ptnr2_symmetry
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_alt_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_atom_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_PDB_ins_code
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_pdbx_struct_conn_angle.value_esd
1 OP2 ? A DG 3 ? A DG 3 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? C HOH . ? A HOH 36 ? 1_555 130.6 ?
2 OP2 ? A DG 3 ? A DG 3 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? C HOH . ? A HOH 45 ? 1_555 99.3 ?
3 O ? C HOH . ? A HOH 36 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? C HOH . ? A HOH 45 ? 1_555 102.8 ?
#
loop_
_pdbx_audit_revision_history.ordinal
_pdbx_audit_revision_history.data_content_type
_pdbx_audit_revision_history.major_revision
_pdbx_audit_revision_history.minor_revision
_pdbx_audit_revision_history.revision_date
1 'Structure model' 1 0 2010-03-09
2 'Structure model' 1 1 2011-07-13
3 'Structure model' 1 2 2012-06-13
4 'Structure model' 1 3 2012-09-26
5 'Structure model' 1 4 2023-09-06
#
_pdbx_audit_revision_details.ordinal 1
_pdbx_audit_revision_details.revision_ordinal 1
_pdbx_audit_revision_details.data_content_type 'Structure model'
_pdbx_audit_revision_details.provider repository
_pdbx_audit_revision_details.type 'Initial release'
_pdbx_audit_revision_details.description ?
_pdbx_audit_revision_details.details ?
#
loop_
_pdbx_audit_revision_group.ordinal
_pdbx_audit_revision_group.revision_ordinal
_pdbx_audit_revision_group.data_content_type
_pdbx_audit_revision_group.group
1 2 'Structure model' Advisory
2 2 'Structure model' 'Version format compliance'
3 3 'Structure model' 'Database references'
4 4 'Structure model' 'Database references'
5 5 'Structure model' 'Data collection'
6 5 'Structure model' 'Database references'
7 5 'Structure model' 'Derived calculations'
8 5 'Structure model' 'Refinement description'
#
loop_
_pdbx_audit_revision_category.ordinal
_pdbx_audit_revision_category.revision_ordinal
_pdbx_audit_revision_category.data_content_type
_pdbx_audit_revision_category.category
1 5 'Structure model' chem_comp_atom
2 5 'Structure model' chem_comp_bond
3 5 'Structure model' database_2
4 5 'Structure model' pdbx_initial_refinement_model
5 5 'Structure model' struct_conn
6 5 'Structure model' struct_site
#
loop_
_pdbx_audit_revision_item.ordinal
_pdbx_audit_revision_item.revision_ordinal
_pdbx_audit_revision_item.data_content_type
_pdbx_audit_revision_item.item
1 5 'Structure model' '_database_2.pdbx_DOI'
2 5 'Structure model' '_database_2.pdbx_database_accession'
3 5 'Structure model' '_struct_conn.conn_type_id'
4 5 'Structure model' '_struct_conn.id'
5 5 'Structure model' '_struct_conn.pdbx_dist_value'
6 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag'
7 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id'
8 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id'
9 5 'Structure model' '_struct_conn.ptnr1_label_atom_id'
10 5 'Structure model' '_struct_conn.ptnr1_label_comp_id'
11 5 'Structure model' '_struct_conn.ptnr1_label_seq_id'
12 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id'
13 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id'
14 5 'Structure model' '_struct_conn.ptnr2_label_asym_id'
15 5 'Structure model' '_struct_conn.ptnr2_label_atom_id'
16 5 'Structure model' '_struct_conn.ptnr2_label_comp_id'
17 5 'Structure model' '_struct_conn.ptnr2_label_seq_id'
18 5 'Structure model' '_struct_site.pdbx_auth_asym_id'
19 5 'Structure model' '_struct_site.pdbx_auth_comp_id'
20 5 'Structure model' '_struct_site.pdbx_auth_seq_id'
#
_pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION'
_pdbx_refine_tls.id 1
_pdbx_refine_tls.details ?
_pdbx_refine_tls.method refined
_pdbx_refine_tls.origin_x 31.5133
_pdbx_refine_tls.origin_y 30.4882
_pdbx_refine_tls.origin_z 2.3842
_pdbx_refine_tls.T[1][1] 0.0169
_pdbx_refine_tls.T[2][2] -0.0057
_pdbx_refine_tls.T[3][3] 0.0077
_pdbx_refine_tls.T[1][2] -0.0065
_pdbx_refine_tls.T[1][3] 0.0054
_pdbx_refine_tls.T[2][3] -0.0025
_pdbx_refine_tls.L[1][1] 0.1824
_pdbx_refine_tls.L[2][2] 1.3050
_pdbx_refine_tls.L[3][3] 0.2928
_pdbx_refine_tls.L[1][2] -0.3805
_pdbx_refine_tls.L[1][3] -0.0034
_pdbx_refine_tls.L[2][3] 0.2072
_pdbx_refine_tls.S[1][1] -0.0049
_pdbx_refine_tls.S[1][2] 0.0122
_pdbx_refine_tls.S[1][3] 0.0094
_pdbx_refine_tls.S[2][1] 0.1295
_pdbx_refine_tls.S[2][2] 0.0189
_pdbx_refine_tls.S[2][3] -0.0139
_pdbx_refine_tls.S[3][1] 0.0248
_pdbx_refine_tls.S[3][2] -0.0403
_pdbx_refine_tls.S[3][3] -0.0140
#
_pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION'
_pdbx_refine_tls_group.id 1
_pdbx_refine_tls_group.refine_tls_id 1
_pdbx_refine_tls_group.beg_auth_asym_id A
_pdbx_refine_tls_group.beg_auth_seq_id 1
_pdbx_refine_tls_group.beg_label_asym_id ?
_pdbx_refine_tls_group.beg_label_seq_id ?
_pdbx_refine_tls_group.end_auth_asym_id A
_pdbx_refine_tls_group.end_auth_seq_id 8
_pdbx_refine_tls_group.end_label_asym_id ?
_pdbx_refine_tls_group.end_label_seq_id ?
_pdbx_refine_tls_group.selection ?
_pdbx_refine_tls_group.selection_details ?
#
loop_
_software.name
_software.classification
_software.version
_software.citation_id
_software.pdbx_ordinal
CBASS 'data collection' . ? 1
PHASES phasing . ? 2
REFMAC refinement 5.2.0019 ? 3
HKL-2000 'data reduction' . ? 4
HKL-2000 'data scaling' . ? 5
#
_pdbx_validate_rmsd_angle.id 1
_pdbx_validate_rmsd_angle.PDB_model_num 1
_pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'"
_pdbx_validate_rmsd_angle.auth_asym_id_1 A
_pdbx_validate_rmsd_angle.auth_comp_id_1 DC
_pdbx_validate_rmsd_angle.auth_seq_id_1 8
_pdbx_validate_rmsd_angle.PDB_ins_code_1 ?
_pdbx_validate_rmsd_angle.label_alt_id_1 ?
_pdbx_validate_rmsd_angle.auth_atom_id_2 "C1'"
_pdbx_validate_rmsd_angle.auth_asym_id_2 A
_pdbx_validate_rmsd_angle.auth_comp_id_2 DC
_pdbx_validate_rmsd_angle.auth_seq_id_2 8
_pdbx_validate_rmsd_angle.PDB_ins_code_2 ?
_pdbx_validate_rmsd_angle.label_alt_id_2 ?
_pdbx_validate_rmsd_angle.auth_atom_id_3 N1
_pdbx_validate_rmsd_angle.auth_asym_id_3 A
_pdbx_validate_rmsd_angle.auth_comp_id_3 DC
_pdbx_validate_rmsd_angle.auth_seq_id_3 8
_pdbx_validate_rmsd_angle.PDB_ins_code_3 ?
_pdbx_validate_rmsd_angle.label_alt_id_3 ?
_pdbx_validate_rmsd_angle.angle_value 110.35
_pdbx_validate_rmsd_angle.angle_target_value 108.30
_pdbx_validate_rmsd_angle.angle_deviation 2.05
_pdbx_validate_rmsd_angle.angle_standard_deviation 0.30
_pdbx_validate_rmsd_angle.linker_flag N
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
DA OP3 O N N 1
DA P P N N 2
DA OP1 O N N 3
DA OP2 O N N 4
DA "O5'" O N N 5
DA "C5'" C N N 6
DA "C4'" C N R 7
DA "O4'" O N N 8
DA "C3'" C N S 9
DA "O3'" O N N 10
DA "C2'" C N N 11
DA "C1'" C N R 12
DA N9 N Y N 13
DA C8 C Y N 14
DA N7 N Y N 15
DA C5 C Y N 16
DA C6 C Y N 17
DA N6 N N N 18
DA N1 N Y N 19
DA C2 C Y N 20
DA N3 N Y N 21
DA C4 C Y N 22
DA HOP3 H N N 23
DA HOP2 H N N 24
DA "H5'" H N N 25
DA "H5''" H N N 26
DA "H4'" H N N 27
DA "H3'" H N N 28
DA "HO3'" H N N 29
DA "H2'" H N N 30
DA "H2''" H N N 31
DA "H1'" H N N 32
DA H8 H N N 33
DA H61 H N N 34
DA H62 H N N 35
DA H2 H N N 36
DC OP3 O N N 37
DC P P N N 38
DC OP1 O N N 39
DC OP2 O N N 40
DC "O5'" O N N 41
DC "C5'" C N N 42
DC "C4'" C N R 43
DC "O4'" O N N 44
DC "C3'" C N S 45
DC "O3'" O N N 46
DC "C2'" C N N 47
DC "C1'" C N R 48
DC N1 N N N 49
DC C2 C N N 50
DC O2 O N N 51
DC N3 N N N 52
DC C4 C N N 53
DC N4 N N N 54
DC C5 C N N 55
DC C6 C N N 56
DC HOP3 H N N 57
DC HOP2 H N N 58
DC "H5'" H N N 59
DC "H5''" H N N 60
DC "H4'" H N N 61
DC "H3'" H N N 62
DC "HO3'" H N N 63
DC "H2'" H N N 64
DC "H2''" H N N 65
DC "H1'" H N N 66
DC H41 H N N 67
DC H42 H N N 68
DC H5 H N N 69
DC H6 H N N 70
DG OP3 O N N 71
DG P P N N 72
DG OP1 O N N 73
DG OP2 O N N 74
DG "O5'" O N N 75
DG "C5'" C N N 76
DG "C4'" C N R 77
DG "O4'" O N N 78
DG "C3'" C N S 79
DG "O3'" O N N 80
DG "C2'" C N N 81
DG "C1'" C N R 82
DG N9 N Y N 83
DG C8 C Y N 84
DG N7 N Y N 85
DG C5 C Y N 86
DG C6 C N N 87
DG O6 O N N 88
DG N1 N N N 89
DG C2 C N N 90
DG N2 N N N 91
DG N3 N N N 92
DG C4 C Y N 93
DG HOP3 H N N 94
DG HOP2 H N N 95
DG "H5'" H N N 96
DG "H5''" H N N 97
DG "H4'" H N N 98
DG "H3'" H N N 99
DG "HO3'" H N N 100
DG "H2'" H N N 101
DG "H2''" H N N 102
DG "H1'" H N N 103
DG H8 H N N 104
DG H1 H N N 105
DG H21 H N N 106
DG H22 H N N 107
HOH O O N N 108
HOH H1 H N N 109
HOH H2 H N N 110
MG MG MG N N 111
UMS OP3 O N N 112
UMS P P N N 113
UMS OP1 O N N 114
UMS OP2 O N N 115
UMS "O5'" O N N 116
UMS "C5'" C N N 117
UMS "C4'" C N R 118
UMS "O4'" O N N 119
UMS "C3'" C N R 120
UMS "O3'" O N N 121
UMS "C2'" C N R 122
UMS "SE2'" SE N N 123
UMS "C1'" C N R 124
UMS "CA'" C N N 125
UMS N1 N N N 126
UMS C2 C N N 127
UMS O2 O N N 128
UMS N3 N N N 129
UMS C4 C N N 130
UMS O4 O N N 131
UMS C5 C N N 132
UMS C6 C N N 133
UMS HOP3 H N N 134
UMS HOP2 H N N 135
UMS "H5'" H N N 136
UMS "H5'2" H N N 137
UMS "H4'" H N N 138
UMS "H3'" H N N 139
UMS "HO3'" H N N 140
UMS "H2'" H N N 141
UMS "H1'" H N N 142
UMS "HA'" H N N 143
UMS "HA'2" H N N 144
UMS "HA'3" H N N 145
UMS H3 H N N 146
UMS H5 H N N 147
UMS H6 H N N 148
US2 P P N N 149
US2 N1 N N N 150
US2 C6 C N N 151
US2 C2 C N N 152
US2 O2 O N N 153
US2 N3 N N N 154
US2 C4 C N N 155
US2 O4 O N N 156
US2 C5 C N N 157
US2 S5 S N N 158
US2 C5A C N N 159
US2 "C1'" C N R 160
US2 "O4'" O N N 161
US2 "C4'" C N R 162
US2 "C3'" C N S 163
US2 "O3'" O N N 164
US2 "C2'" C N N 165
US2 "C5'" C N N 166
US2 "O5'" O N N 167
US2 O1P O N N 168
US2 O2P O N N 169
US2 H6 H N N 170
US2 HN3 H N N 171
US2 H15A H N N 172
US2 H25A H N N 173
US2 H35A H N N 174
US2 "H1'" H N N 175
US2 "H4'" H N N 176
US2 "H3'" H N N 177
US2 "HO3'" H N N 178
US2 "H12'" H N N 179
US2 "H22'" H N N 180
US2 "H15'" H N N 181
US2 "H25'" H N N 182
US2 O3P O N N 183
US2 HO2P H N N 184
US2 HO3P H N N 185
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
DA OP3 P sing N N 1
DA OP3 HOP3 sing N N 2
DA P OP1 doub N N 3
DA P OP2 sing N N 4
DA P "O5'" sing N N 5
DA OP2 HOP2 sing N N 6
DA "O5'" "C5'" sing N N 7
DA "C5'" "C4'" sing N N 8
DA "C5'" "H5'" sing N N 9
DA "C5'" "H5''" sing N N 10
DA "C4'" "O4'" sing N N 11
DA "C4'" "C3'" sing N N 12
DA "C4'" "H4'" sing N N 13
DA "O4'" "C1'" sing N N 14
DA "C3'" "O3'" sing N N 15
DA "C3'" "C2'" sing N N 16
DA "C3'" "H3'" sing N N 17
DA "O3'" "HO3'" sing N N 18
DA "C2'" "C1'" sing N N 19
DA "C2'" "H2'" sing N N 20
DA "C2'" "H2''" sing N N 21
DA "C1'" N9 sing N N 22
DA "C1'" "H1'" sing N N 23
DA N9 C8 sing Y N 24
DA N9 C4 sing Y N 25
DA C8 N7 doub Y N 26
DA C8 H8 sing N N 27
DA N7 C5 sing Y N 28
DA C5 C6 sing Y N 29
DA C5 C4 doub Y N 30
DA C6 N6 sing N N 31
DA C6 N1 doub Y N 32
DA N6 H61 sing N N 33
DA N6 H62 sing N N 34
DA N1 C2 sing Y N 35
DA C2 N3 doub Y N 36
DA C2 H2 sing N N 37
DA N3 C4 sing Y N 38
DC OP3 P sing N N 39
DC OP3 HOP3 sing N N 40
DC P OP1 doub N N 41
DC P OP2 sing N N 42
DC P "O5'" sing N N 43
DC OP2 HOP2 sing N N 44
DC "O5'" "C5'" sing N N 45
DC "C5'" "C4'" sing N N 46
DC "C5'" "H5'" sing N N 47
DC "C5'" "H5''" sing N N 48
DC "C4'" "O4'" sing N N 49
DC "C4'" "C3'" sing N N 50
DC "C4'" "H4'" sing N N 51
DC "O4'" "C1'" sing N N 52
DC "C3'" "O3'" sing N N 53
DC "C3'" "C2'" sing N N 54
DC "C3'" "H3'" sing N N 55
DC "O3'" "HO3'" sing N N 56
DC "C2'" "C1'" sing N N 57
DC "C2'" "H2'" sing N N 58
DC "C2'" "H2''" sing N N 59
DC "C1'" N1 sing N N 60
DC "C1'" "H1'" sing N N 61
DC N1 C2 sing N N 62
DC N1 C6 sing N N 63
DC C2 O2 doub N N 64
DC C2 N3 sing N N 65
DC N3 C4 doub N N 66
DC C4 N4 sing N N 67
DC C4 C5 sing N N 68
DC N4 H41 sing N N 69
DC N4 H42 sing N N 70
DC C5 C6 doub N N 71
DC C5 H5 sing N N 72
DC C6 H6 sing N N 73
DG OP3 P sing N N 74
DG OP3 HOP3 sing N N 75
DG P OP1 doub N N 76
DG P OP2 sing N N 77
DG P "O5'" sing N N 78
DG OP2 HOP2 sing N N 79
DG "O5'" "C5'" sing N N 80
DG "C5'" "C4'" sing N N 81
DG "C5'" "H5'" sing N N 82
DG "C5'" "H5''" sing N N 83
DG "C4'" "O4'" sing N N 84
DG "C4'" "C3'" sing N N 85
DG "C4'" "H4'" sing N N 86
DG "O4'" "C1'" sing N N 87
DG "C3'" "O3'" sing N N 88
DG "C3'" "C2'" sing N N 89
DG "C3'" "H3'" sing N N 90
DG "O3'" "HO3'" sing N N 91
DG "C2'" "C1'" sing N N 92
DG "C2'" "H2'" sing N N 93
DG "C2'" "H2''" sing N N 94
DG "C1'" N9 sing N N 95
DG "C1'" "H1'" sing N N 96
DG N9 C8 sing Y N 97
DG N9 C4 sing Y N 98
DG C8 N7 doub Y N 99
DG C8 H8 sing N N 100
DG N7 C5 sing Y N 101
DG C5 C6 sing N N 102
DG C5 C4 doub Y N 103
DG C6 O6 doub N N 104
DG C6 N1 sing N N 105
DG N1 C2 sing N N 106
DG N1 H1 sing N N 107
DG C2 N2 sing N N 108
DG C2 N3 doub N N 109
DG N2 H21 sing N N 110
DG N2 H22 sing N N 111
DG N3 C4 sing N N 112
HOH O H1 sing N N 113
HOH O H2 sing N N 114
UMS OP3 P sing N N 115
UMS OP3 HOP3 sing N N 116
UMS P OP1 doub N N 117
UMS P OP2 sing N N 118
UMS P "O5'" sing N N 119
UMS OP2 HOP2 sing N N 120
UMS "O5'" "C5'" sing N N 121
UMS "C5'" "C4'" sing N N 122
UMS "C5'" "H5'" sing N N 123
UMS "C5'" "H5'2" sing N N 124
UMS "C4'" "O4'" sing N N 125
UMS "C4'" "C3'" sing N N 126
UMS "C4'" "H4'" sing N N 127
UMS "O4'" "C1'" sing N N 128
UMS "C3'" "O3'" sing N N 129
UMS "C3'" "C2'" sing N N 130
UMS "C3'" "H3'" sing N N 131
UMS "O3'" "HO3'" sing N N 132
UMS "C2'" "SE2'" sing N N 133
UMS "C2'" "C1'" sing N N 134
UMS "C2'" "H2'" sing N N 135
UMS "SE2'" "CA'" sing N N 136
UMS "C1'" N1 sing N N 137
UMS "C1'" "H1'" sing N N 138
UMS "CA'" "HA'" sing N N 139
UMS "CA'" "HA'2" sing N N 140
UMS "CA'" "HA'3" sing N N 141
UMS N1 C2 sing N N 142
UMS N1 C6 sing N N 143
UMS C2 O2 doub N N 144
UMS C2 N3 sing N N 145
UMS N3 C4 sing N N 146
UMS N3 H3 sing N N 147
UMS C4 O4 doub N N 148
UMS C4 C5 sing N N 149
UMS C5 C6 doub N N 150
UMS C5 H5 sing N N 151
UMS C6 H6 sing N N 152
US2 P O2P sing N N 153
US2 N1 C6 sing N N 154
US2 N1 "C1'" sing N N 155
US2 C6 H6 sing N N 156
US2 C2 N1 sing N N 157
US2 O2 C2 doub N N 158
US2 N3 C4 sing N N 159
US2 N3 C2 sing N N 160
US2 N3 HN3 sing N N 161
US2 C4 C5 sing N N 162
US2 O4 C4 doub N N 163
US2 C5 S5 sing N N 164
US2 C5 C6 doub N N 165
US2 S5 C5A sing N N 166
US2 C5A H15A sing N N 167
US2 C5A H25A sing N N 168
US2 C5A H35A sing N N 169
US2 "C1'" "O4'" sing N N 170
US2 "C1'" "C2'" sing N N 171
US2 "C1'" "H1'" sing N N 172
US2 "O4'" "C4'" sing N N 173
US2 "C4'" "C3'" sing N N 174
US2 "C4'" "C5'" sing N N 175
US2 "C4'" "H4'" sing N N 176
US2 "C3'" "O3'" sing N N 177
US2 "C3'" "H3'" sing N N 178
US2 "O3'" "HO3'" sing N N 179
US2 "C2'" "C3'" sing N N 180
US2 "C2'" "H12'" sing N N 181
US2 "C2'" "H22'" sing N N 182
US2 "C5'" "H15'" sing N N 183
US2 "C5'" "H25'" sing N N 184
US2 "O5'" "C5'" sing N N 185
US2 "O5'" P sing N N 186
US2 O1P P doub N N 187
US2 P O3P sing N N 188
US2 O2P HO2P sing N N 189
US2 O3P HO3P sing N N 190
#
loop_
_ndb_struct_conf_na.entry_id
_ndb_struct_conf_na.feature
3IKI 'a-form double helix'
3IKI 'internal loop'
#
loop_
_ndb_struct_na_base_pair.model_number
_ndb_struct_na_base_pair.i_label_asym_id
_ndb_struct_na_base_pair.i_label_comp_id
_ndb_struct_na_base_pair.i_label_seq_id
_ndb_struct_na_base_pair.i_symmetry
_ndb_struct_na_base_pair.j_label_asym_id
_ndb_struct_na_base_pair.j_label_comp_id
_ndb_struct_na_base_pair.j_label_seq_id
_ndb_struct_na_base_pair.j_symmetry
_ndb_struct_na_base_pair.shear
_ndb_struct_na_base_pair.stretch
_ndb_struct_na_base_pair.stagger
_ndb_struct_na_base_pair.buckle
_ndb_struct_na_base_pair.propeller
_ndb_struct_na_base_pair.opening
_ndb_struct_na_base_pair.pair_number
_ndb_struct_na_base_pair.pair_name
_ndb_struct_na_base_pair.i_auth_asym_id
_ndb_struct_na_base_pair.i_auth_seq_id
_ndb_struct_na_base_pair.i_PDB_ins_code
_ndb_struct_na_base_pair.j_auth_asym_id
_ndb_struct_na_base_pair.j_auth_seq_id
_ndb_struct_na_base_pair.j_PDB_ins_code
_ndb_struct_na_base_pair.hbond_type_28
_ndb_struct_na_base_pair.hbond_type_12
1 A DG 1 1_555 A DC 8 7_555 -0.350 -0.123 -0.340 -19.369 -13.573 -2.360 1 A_DG1:DC8_A A 1 ? A 8 ? 19 1
1 A UMS 2 1_555 A DA 7 7_555 -0.037 -0.094 0.142 -5.623 -11.049 2.831 2 A_UMS2:DA7_A A 2 ? A 7 ? 20 1
1 A DG 3 1_555 A DC 6 7_555 -0.255 -0.231 0.247 -4.548 -13.598 -0.012 3 A_DG3:DC6_A A 3 ? A 6 ? 19 1
1 A DG 1 1_555 A DC 8 1_555 -0.350 -0.123 -0.340 -19.369 -13.573 -2.360 4 A_DG1:DC8_A A 1 ? A 8 ? 19 1
1 A UMS 2 1_555 A DA 7 1_555 -0.037 -0.094 0.142 -5.623 -11.049 2.831 5 A_UMS2:DA7_A A 2 ? A 7 ? 20 1
1 A DG 3 1_555 A DC 6 1_555 -0.255 -0.231 0.247 -4.548 -13.598 -0.012 6 A_DG3:DC6_A A 3 ? A 6 ? 19 1
#
loop_
_ndb_struct_na_base_pair_step.model_number
_ndb_struct_na_base_pair_step.i_label_asym_id_1
_ndb_struct_na_base_pair_step.i_label_comp_id_1
_ndb_struct_na_base_pair_step.i_label_seq_id_1
_ndb_struct_na_base_pair_step.i_symmetry_1
_ndb_struct_na_base_pair_step.j_label_asym_id_1
_ndb_struct_na_base_pair_step.j_label_comp_id_1
_ndb_struct_na_base_pair_step.j_label_seq_id_1
_ndb_struct_na_base_pair_step.j_symmetry_1
_ndb_struct_na_base_pair_step.i_label_asym_id_2
_ndb_struct_na_base_pair_step.i_label_comp_id_2
_ndb_struct_na_base_pair_step.i_label_seq_id_2
_ndb_struct_na_base_pair_step.i_symmetry_2
_ndb_struct_na_base_pair_step.j_label_asym_id_2
_ndb_struct_na_base_pair_step.j_label_comp_id_2
_ndb_struct_na_base_pair_step.j_label_seq_id_2
_ndb_struct_na_base_pair_step.j_symmetry_2
_ndb_struct_na_base_pair_step.shift
_ndb_struct_na_base_pair_step.slide
_ndb_struct_na_base_pair_step.rise
_ndb_struct_na_base_pair_step.tilt
_ndb_struct_na_base_pair_step.roll
_ndb_struct_na_base_pair_step.twist
_ndb_struct_na_base_pair_step.x_displacement
_ndb_struct_na_base_pair_step.y_displacement
_ndb_struct_na_base_pair_step.helical_rise
_ndb_struct_na_base_pair_step.inclination
_ndb_struct_na_base_pair_step.tip
_ndb_struct_na_base_pair_step.helical_twist
_ndb_struct_na_base_pair_step.step_number
_ndb_struct_na_base_pair_step.step_name
_ndb_struct_na_base_pair_step.i_auth_asym_id_1
_ndb_struct_na_base_pair_step.i_auth_seq_id_1
_ndb_struct_na_base_pair_step.i_PDB_ins_code_1
_ndb_struct_na_base_pair_step.j_auth_asym_id_1
_ndb_struct_na_base_pair_step.j_auth_seq_id_1
_ndb_struct_na_base_pair_step.j_PDB_ins_code_1
_ndb_struct_na_base_pair_step.i_auth_asym_id_2
_ndb_struct_na_base_pair_step.i_auth_seq_id_2
_ndb_struct_na_base_pair_step.i_PDB_ins_code_2
_ndb_struct_na_base_pair_step.j_auth_asym_id_2
_ndb_struct_na_base_pair_step.j_auth_seq_id_2
_ndb_struct_na_base_pair_step.j_PDB_ins_code_2
1 A DG 1 1_555 A DC 8 7_555 A UMS 2 1_555 A DA 7 7_555 0.539 -0.832 3.040 -2.846 13.421 30.709 -3.364 -1.341 2.419 23.902 5.068
33.567 1 AA_DG1UMS2:DA7DC8_AA A 1 ? A 8 ? A 2 ? A 7 ?
1 A UMS 2 1_555 A DA 7 7_555 A DG 3 1_555 A DC 6 7_555 0.694 -1.478 3.075 0.004 11.978 28.509 -4.762 -1.303 2.283 23.076 -0.008
30.875 2 AA_UMS2DG3:DC6DA7_AA A 2 ? A 7 ? A 3 ? A 6 ?
1 A DG 1 1_555 A DC 8 1_555 A UMS 2 1_555 A DA 7 1_555 0.539 -0.832 3.040 -2.846 13.421 30.709 -3.364 -1.341 2.419 23.902 5.068
33.567 3 AA_DG1UMS2:DA7DC8_AA A 1 ? A 8 ? A 2 ? A 7 ?
1 A UMS 2 1_555 A DA 7 1_555 A DG 3 1_555 A DC 6 1_555 0.694 -1.478 3.075 0.004 11.978 28.509 -4.762 -1.303 2.283 23.076 -0.008
30.875 4 AA_UMS2DG3:DC6DA7_AA A 2 ? A 7 ? A 3 ? A 6 ?
#
loop_
_pdbx_entity_nonpoly.entity_id
_pdbx_entity_nonpoly.name
_pdbx_entity_nonpoly.comp_id
2 'MAGNESIUM ION' MG
3 water HOH
#
_pdbx_initial_refinement_model.id 1
_pdbx_initial_refinement_model.entity_id_list ?
_pdbx_initial_refinement_model.type 'experimental model'
_pdbx_initial_refinement_model.source_name PDB
_pdbx_initial_refinement_model.accession_code 1DNS
_pdbx_initial_refinement_model.details ?
#