data_3IJK
#
_entry.id 3IJK
#
_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 3IJK pdb_00003ijk 10.2210/pdb3ijk/pdb
NDB NA0115 ? ?
RCSB RCSB054491 ? ?
WWPDB D_1000054491 ? ?
#
_pdbx_database_related.db_name PDB
_pdbx_database_related.db_id 3IJN
_pdbx_database_related.details .
_pdbx_database_related.content_type unspecified
#
_pdbx_database_status.status_code REL
_pdbx_database_status.entry_id 3IJK
_pdbx_database_status.recvd_initial_deposition_date 2009-08-04
_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.pdb_format_compatible Y
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.status_code_nmr_data ?
_pdbx_database_status.methods_development_category ?
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Sheng, J.' 1
'Zhang, W.' 2
'Hassan, A.E.A.' 3
'Gan, J.' 4
'Huang, Z.' 5
#
_citation.id primary
_citation.title 'Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate'
_citation.journal_abbrev Chemistryselect
_citation.journal_volume 8
_citation.page_first ?
_citation.page_last ?
_citation.year 2023
_citation.journal_id_ASTM ?
_citation.country DE
_citation.journal_id_ISSN 2365-6549
_citation.journal_id_CSD ?
_citation.book_publisher ?
_citation.pdbx_database_id_PubMed ?
_citation.pdbx_database_id_DOI 10.1002/slct.202302253
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Fang, Z.' 1 ?
primary 'Dantsu, Y.' 2 ?
primary 'Chen, C.' 3 ?
primary 'Zhang, W.' 4 ?
primary 'Huang, Z.' 5 ?
#
_cell.entry_id 3IJK
_cell.length_a 43.210
_cell.length_b 43.210
_cell.length_c 23.692
_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 3IJK
_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*(T5O)P*AP*CP*AP*C)-3'" 2521.577 1 ? ? ? '5-OMe modified DNA octamer'
2 water nat water 18.015 30 ? ? ? ?
#
_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)(T5O)(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 T5O 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 'synthetic construct'
_pdbx_entity_src_syn.organism_common_name ?
_pdbx_entity_src_syn.ncbi_taxonomy_id 32630
_pdbx_entity_src_syn.details ?
#
_struct_ref.id 1
_struct_ref.db_name PDB
_struct_ref.db_code 3IJK
_struct_ref.pdbx_db_accession 3IJK
_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 3IJK
_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 3IJK
_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
T5O 'DNA linking' n
;2'-deoxy-5-methoxyuridine 5'-(dihydrogen phosphate)
;
"5-methoxy-2'-deoxyuridine-5'-phosphate" 'C10 H15 N2 O9 P' 338.208
UMS 'DNA linking' n "2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE" ?
'C10 H15 N2 O8 P Se' 401.168
#
_exptl.entry_id 3IJK
_exptl.method 'X-RAY DIFFRACTION'
_exptl.crystals_number 1
#
_exptl_crystal.id 1
_exptl_crystal.density_meas ?
_exptl_crystal.density_Matthews 2.19
_exptl_crystal.density_percent_sol 43.91
_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 6.0
_exptl_crystal_grow.pdbx_details
;10% v / v MPD, 40 mM Na Cacodylate pH 6.0, 12 mM Spermine tetra-HCl, 80 mM Strontium 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 210'
_diffrn_detector.pdbx_collection_date 2009-07-14
_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 'Si(111) channel-cut crystal 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 X12C'
_diffrn_source.pdbx_synchrotron_site NSLS
_diffrn_source.pdbx_synchrotron_beamline X12C
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_wavelength_list 0.9795
#
_reflns.entry_id 3IJK
_reflns.observed_criterion_sigma_I ?
_reflns.observed_criterion_sigma_F ?
_reflns.d_resolution_low 50
_reflns.d_resolution_high 1.30
_reflns.number_obs 5561
_reflns.number_all 10495
_reflns.percent_possible_obs 94.5
_reflns.pdbx_Rmerge_I_obs 0.037
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_sigmaI 38.35
_reflns.B_iso_Wilson_estimate ?
_reflns.pdbx_redundancy 12.7
_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 1.30
_reflns_shell.d_res_low 1.32
_reflns_shell.percent_possible_all 50.8
_reflns_shell.Rmerge_I_obs 0.682
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.meanI_over_sigI_obs 1
_reflns_shell.pdbx_redundancy 2.0
_reflns_shell.percent_possible_obs ?
_reflns_shell.number_unique_all 264
_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 3IJK
_refine.ls_number_reflns_obs 5301
_refine.ls_number_reflns_all 5574
_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 30.56
_refine.ls_d_res_high 1.30
_refine.ls_percent_reflns_obs 95.11
_refine.ls_R_factor_obs ?
_refine.ls_R_factor_all 0.19769
_refine.ls_R_factor_R_work 0.19672
_refine.ls_R_factor_R_free 0.21884
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_percent_reflns_R_free 4.6
_refine.ls_number_reflns_R_free 256
_refine.ls_number_parameters ?
_refine.ls_number_restraints ?
_refine.occupancy_min ?
_refine.occupancy_max ?
_refine.correlation_coeff_Fo_to_Fc 0.964
_refine.correlation_coeff_Fo_to_Fc_free 0.951
_refine.B_iso_mean 12.795
_refine.aniso_B[1][1] -0.09
_refine.aniso_B[2][2] -0.09
_refine.aniso_B[3][3] 0.17
_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 SAD
_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 0.055
_refine.pdbx_overall_ESU_R_Free 0.056
_refine.overall_SU_ML 0.033
_refine.overall_SU_B 1.656
_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 3IJK
_refine_analyze.Luzzati_coordinate_error_obs 0.055
_refine_analyze.Luzzati_sigma_a_obs ?
_refine_analyze.Luzzati_d_res_low_obs ?
_refine_analyze.Luzzati_coordinate_error_free 0.056
_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 0
_refine_hist.number_atoms_solvent 30
_refine_hist.number_atoms_total 193
_refine_hist.d_res_high 1.30
_refine_hist.d_res_low 30.56
#
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 0.006 0.021 ? 180 'X-RAY DIFFRACTION' ?
r_angle_refined_deg 1.600 3.000 ? 270 'X-RAY DIFFRACTION' ?
r_chiral_restr 0.068 0.200 ? 31 'X-RAY DIFFRACTION' ?
r_gen_planes_refined 0.008 0.020 ? 83 'X-RAY DIFFRACTION' ?
r_nbd_refined 0.360 0.200 ? 69 'X-RAY DIFFRACTION' ?
r_nbtor_refined 0.282 0.200 ? 106 'X-RAY DIFFRACTION' ?
r_xyhbond_nbd_refined 0.106 0.200 ? 20 'X-RAY DIFFRACTION' ?
r_symmetry_vdw_refined 0.194 0.200 ? 21 'X-RAY DIFFRACTION' ?
r_symmetry_hbond_refined 0.071 0.200 ? 11 'X-RAY DIFFRACTION' ?
r_scbond_it 0.832 3.000 ? 259 'X-RAY DIFFRACTION' ?
r_scangle_it 1.272 4.500 ? 270 'X-RAY DIFFRACTION' ?
#
_refine_ls_shell.pdbx_total_number_of_bins_used 20
_refine_ls_shell.d_res_high 1.303
_refine_ls_shell.d_res_low 1.336
_refine_ls_shell.number_reflns_R_work 249
_refine_ls_shell.R_factor_R_work 0.470
_refine_ls_shell.percent_reflns_obs 62.04
_refine_ls_shell.R_factor_R_free 0.426
_refine_ls_shell.R_factor_R_free_error ?
_refine_ls_shell.percent_reflns_R_free ?
_refine_ls_shell.number_reflns_R_free 6
_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 3IJK
_struct.title '5-OMe modified DNA 8mer'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 3IJK
_struct_keywords.pdbx_keywords DNA
_struct_keywords.text 'selenium, DNA, 5-methoxy-uridine'
#
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 ?
#
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 ? ? ? ? ? ? ? 1.602 ? ?
covale2 covale both ? A UMS 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A UMS 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.607 ? ?
covale3 covale one ? A DG 3 "O3'" ? ? ? 1_555 A T5O 4 P ? ? A DG 3 A T5O 4 1_555 ? ? ? ? ? ? ? 1.601 ? ?
covale4 covale one ? A T5O 4 "O3'" ? ? ? 1_555 A DA 5 P ? ? A T5O 4 A DA 5 1_555 ? ? ? ? ? ? ? 1.598 ? ?
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 T5O 4 N3 ? ? ? 1_555 A DA 5 N1 ? ? A T5O 4 A DA 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog10 hydrog ? ? A T5O 4 O4 ? ? ? 1_555 A DA 5 N6 ? ? A T5O 4 A DA 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A T5O 4 N3 ? ? A DA 5 A T5O 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A T5O 4 O4 ? ? A DA 5 A T5O 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog13 hydrog ? ? A DC 6 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog14 hydrog ? ? A DC 6 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog15 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 6 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 A UMS 2 N3 ? ? A DA 7 A UMS 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 A UMS 2 O4 ? ? A DA 7 A UMS 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 8 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 8 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog20 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 ? ?
hydrog ? ?
#
_database_PDB_matrix.entry_id 3IJK
_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 3IJK
_atom_sites.fract_transf_matrix[1][1] 0.023143
_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] 0.023143
_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] 0.042208
_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
N
O
P
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 ? 13.561 24.464 -5.219 1.00 12.21 ? 1 DG A "O5'" 1
ATOM 2 C "C5'" . DG A 1 1 ? 13.591 25.852 -4.922 1.00 10.75 ? 1 DG A "C5'" 1
ATOM 3 C "C4'" . DG A 1 1 ? 12.310 26.305 -4.249 1.00 10.71 ? 1 DG A "C4'" 1
ATOM 4 O "O4'" . DG A 1 1 ? 11.170 26.064 -5.117 1.00 10.27 ? 1 DG A "O4'" 1
ATOM 5 C "C3'" . DG A 1 1 ? 11.947 25.585 -2.958 1.00 10.48 ? 1 DG A "C3'" 1
ATOM 6 O "O3'" . DG A 1 1 ? 12.661 26.154 -1.869 1.00 11.95 ? 1 DG A "O3'" 1
ATOM 7 C "C2'" . DG A 1 1 ? 10.450 25.866 -2.877 1.00 10.91 ? 1 DG A "C2'" 1
ATOM 8 C "C1'" . DG A 1 1 ? 10.047 25.698 -4.338 1.00 11.13 ? 1 DG A "C1'" 1
ATOM 9 N N9 . DG A 1 1 ? 9.696 24.314 -4.654 1.00 10.79 ? 1 DG A N9 1
ATOM 10 C C8 . DG A 1 1 ? 10.487 23.383 -5.290 1.00 11.10 ? 1 DG A C8 1
ATOM 11 N N7 . DG A 1 1 ? 9.913 22.221 -5.423 1.00 11.00 ? 1 DG A N7 1
ATOM 12 C C5 . DG A 1 1 ? 8.664 22.390 -4.840 1.00 11.00 ? 1 DG A C5 1
ATOM 13 C C6 . DG A 1 1 ? 7.591 21.477 -4.687 1.00 11.31 ? 1 DG A C6 1
ATOM 14 O O6 . DG A 1 1 ? 7.539 20.294 -5.055 1.00 11.82 ? 1 DG A O6 1
ATOM 15 N N1 . DG A 1 1 ? 6.498 22.048 -4.032 1.00 10.96 ? 1 DG A N1 1
ATOM 16 C C2 . DG A 1 1 ? 6.447 23.348 -3.589 1.00 11.13 ? 1 DG A C2 1
ATOM 17 N N2 . DG A 1 1 ? 5.316 23.733 -2.985 1.00 11.82 ? 1 DG A N2 1
ATOM 18 N N3 . DG A 1 1 ? 7.442 24.214 -3.724 1.00 11.12 ? 1 DG A N3 1
ATOM 19 C C4 . DG A 1 1 ? 8.517 23.670 -4.352 1.00 10.72 ? 1 DG A C4 1
HETATM 20 P P . UMS A 1 2 ? 13.153 25.243 -0.647 1.00 11.68 ? 2 UMS A P 1
HETATM 21 O OP1 . UMS A 1 2 ? 13.980 26.114 0.208 1.00 12.85 ? 2 UMS A OP1 1
HETATM 22 O OP2 . UMS A 1 2 ? 13.711 23.972 -1.156 1.00 12.29 ? 2 UMS A OP2 1
HETATM 23 O "O5'" . UMS A 1 2 ? 11.806 24.873 0.120 1.00 11.26 ? 2 UMS A "O5'" 1
HETATM 24 C "C5'" . UMS A 1 2 ? 11.124 25.875 0.858 1.00 11.74 ? 2 UMS A "C5'" 1
HETATM 25 C "C4'" . UMS A 1 2 ? 9.762 25.376 1.288 1.00 11.93 ? 2 UMS A "C4'" 1
HETATM 26 O "O4'" . UMS A 1 2 ? 8.983 25.022 0.120 1.00 10.85 ? 2 UMS A "O4'" 1
HETATM 27 C "C3'" . UMS A 1 2 ? 9.777 24.088 2.095 1.00 13.43 ? 2 UMS A "C3'" 1
HETATM 28 O "O3'" . UMS A 1 2 ? 10.146 24.309 3.438 1.00 16.18 ? 2 UMS A "O3'" 1
HETATM 29 C "C2'" . UMS A 1 2 ? 8.327 23.653 1.934 1.00 12.54 ? 2 UMS A "C2'" 1
HETATM 30 SE "SE2'" . UMS A 1 2 ? 7.084 24.724 3.023 0.90 14.59 ? 2 UMS A "SE2'" 1
HETATM 31 C "C1'" . UMS A 1 2 ? 8.141 23.930 0.443 1.00 11.32 ? 2 UMS A "C1'" 1
HETATM 32 C "CA'" . UMS A 1 2 ? 5.410 23.716 2.883 0.90 12.62 ? 2 UMS A "CA'" 1
HETATM 33 N N1 . UMS A 1 2 ? 8.518 22.733 -0.382 1.00 10.87 ? 2 UMS A N1 1
HETATM 34 C C2 . UMS A 1 2 ? 7.608 21.698 -0.478 1.00 11.06 ? 2 UMS A C2 1
HETATM 35 O O2 . UMS A 1 2 ? 6.525 21.723 0.072 1.00 11.88 ? 2 UMS A O2 1
HETATM 36 N N3 . UMS A 1 2 ? 8.015 20.638 -1.250 1.00 11.25 ? 2 UMS A N3 1
HETATM 37 C C4 . UMS A 1 2 ? 9.228 20.501 -1.905 1.00 10.88 ? 2 UMS A C4 1
HETATM 38 O O4 . UMS A 1 2 ? 9.451 19.487 -2.551 1.00 11.33 ? 2 UMS A O4 1
HETATM 39 C C5 . UMS A 1 2 ? 10.135 21.615 -1.751 1.00 10.84 ? 2 UMS A C5 1
HETATM 40 C C6 . UMS A 1 2 ? 9.753 22.662 -1.010 1.00 10.96 ? 2 UMS A C6 1
ATOM 41 P P . DG A 1 3 ? 11.025 23.209 4.212 1.00 18.48 ? 3 DG A P 1
ATOM 42 O OP1 . DG A 1 3 ? 11.437 23.850 5.466 1.00 19.85 ? 3 DG A OP1 1
ATOM 43 O OP2 . DG A 1 3 ? 12.042 22.643 3.295 1.00 20.03 ? 3 DG A OP2 1
ATOM 44 O "O5'" . DG A 1 3 ? 9.994 22.022 4.524 1.00 18.08 ? 3 DG A "O5'" 1
ATOM 45 C "C5'" . DG A 1 3 ? 8.890 22.180 5.395 1.00 16.39 ? 3 DG A "C5'" 1
ATOM 46 C "C4'" . DG A 1 3 ? 7.809 21.160 5.069 1.00 14.67 ? 3 DG A "C4'" 1
ATOM 47 O "O4'" . DG A 1 3 ? 7.567 21.125 3.644 1.00 13.85 ? 3 DG A "O4'" 1
ATOM 48 C "C3'" . DG A 1 3 ? 8.125 19.707 5.362 1.00 14.22 ? 3 DG A "C3'" 1
ATOM 49 O "O3'" . DG A 1 3 ? 8.017 19.357 6.800 1.00 12.44 ? 3 DG A "O3'" 1
ATOM 50 C "C2'" . DG A 1 3 ? 7.047 19.017 4.543 1.00 13.44 ? 3 DG A "C2'" 1
ATOM 51 C "C1'" . DG A 1 3 ? 7.097 19.845 3.267 1.00 12.03 ? 3 DG A "C1'" 1
ATOM 52 N N9 . DG A 1 3 ? 7.983 19.262 2.264 1.00 11.49 ? 3 DG A N9 1
ATOM 53 C C8 . DG A 1 3 ? 9.214 19.711 1.840 1.00 11.42 ? 3 DG A C8 1
ATOM 54 N N7 . DG A 1 3 ? 9.749 18.952 0.925 1.00 10.96 ? 3 DG A N7 1
ATOM 55 C C5 . DG A 1 3 ? 8.816 17.939 0.723 1.00 10.81 ? 3 DG A C5 1
ATOM 56 C C6 . DG A 1 3 ? 8.829 16.816 -0.146 1.00 10.99 ? 3 DG A C6 1
ATOM 57 O O6 . DG A 1 3 ? 9.701 16.484 -0.952 1.00 10.97 ? 3 DG A O6 1
ATOM 58 N N1 . DG A 1 3 ? 7.680 16.034 -0.034 1.00 10.71 ? 3 DG A N1 1
ATOM 59 C C2 . DG A 1 3 ? 6.643 16.300 0.824 1.00 10.87 ? 3 DG A C2 1
ATOM 60 N N2 . DG A 1 3 ? 5.615 15.447 0.806 1.00 10.89 ? 3 DG A N2 1
ATOM 61 N N3 . DG A 1 3 ? 6.615 17.342 1.646 1.00 10.66 ? 3 DG A N3 1
ATOM 62 C C4 . DG A 1 3 ? 7.726 18.116 1.542 1.00 10.53 ? 3 DG A C4 1
HETATM 63 P P . T5O A 1 4 ? 8.625 18.044 7.485 1.00 12.47 ? 4 T5O A P 1
HETATM 64 N N1 . T5O A 1 4 ? 7.819 14.270 3.369 1.00 9.08 ? 4 T5O A N1 1
HETATM 65 C C2 . T5O A 1 4 ? 7.974 13.326 2.376 1.00 8.33 ? 4 T5O A C2 1
HETATM 66 O O2 . T5O A 1 4 ? 7.151 12.477 2.132 1.00 7.86 ? 4 T5O A O2 1
HETATM 67 N N3 . T5O A 1 4 ? 9.133 13.405 1.661 1.00 7.58 ? 4 T5O A N3 1
HETATM 68 C C4 . T5O A 1 4 ? 10.150 14.311 1.865 1.00 9.26 ? 4 T5O A C4 1
HETATM 69 O O4 . T5O A 1 4 ? 11.169 14.309 1.189 1.00 8.29 ? 4 T5O A O4 1
HETATM 70 C C5 . T5O A 1 4 ? 9.949 15.274 2.922 1.00 9.39 ? 4 T5O A C5 1
HETATM 71 O O5 . T5O A 1 4 ? 11.002 16.217 3.119 1.00 10.77 ? 4 T5O A O5 1
HETATM 72 C C6 . T5O A 1 4 ? 8.805 15.218 3.620 1.00 8.97 ? 4 T5O A C6 1
HETATM 73 C "C1'" . T5O A 1 4 ? 6.549 14.221 4.187 1.00 8.88 ? 4 T5O A "C1'" 1
HETATM 74 C "C2'" . T5O A 1 4 ? 6.622 13.185 5.311 1.00 8.86 ? 4 T5O A "C2'" 1
HETATM 75 O OP2 . T5O A 1 4 ? 10.059 17.982 7.187 1.00 10.00 ? 4 T5O A OP2 1
HETATM 76 C "C3'" . T5O A 1 4 ? 7.060 14.042 6.495 1.00 8.87 ? 4 T5O A "C3'" 1
HETATM 77 O "O3'" . T5O A 1 4 ? 6.737 13.494 7.766 1.00 9.46 ? 4 T5O A "O3'" 1
HETATM 78 C "C4'" . T5O A 1 4 ? 6.180 15.254 6.228 1.00 8.87 ? 4 T5O A "C4'" 1
HETATM 79 O "O4'" . T5O A 1 4 ? 6.310 15.470 4.802 1.00 9.01 ? 4 T5O A "O4'" 1
HETATM 80 C "C5'" . T5O A 1 4 ? 6.569 16.508 6.980 1.00 10.56 ? 4 T5O A "C5'" 1
HETATM 81 O "O5'" . T5O A 1 4 ? 7.940 16.802 6.753 1.00 11.45 ? 4 T5O A "O5'" 1
HETATM 82 C C7 . T5O A 1 4 ? 10.727 17.150 4.165 1.00 11.33 ? 4 T5O A C7 1
HETATM 83 O OP1 . T5O A 1 4 ? 8.178 18.049 8.896 1.00 13.34 ? 4 T5O A OP1 1
ATOM 84 P P . DA A 1 5 ? 7.691 12.447 8.506 1.00 10.14 ? 5 DA A P 1
ATOM 85 O OP1 . DA A 1 5 ? 7.214 12.417 9.944 1.00 13.73 ? 5 DA A OP1 1
ATOM 86 O OP2 . DA A 1 5 ? 9.142 12.719 8.281 1.00 15.09 ? 5 DA A OP2 1
ATOM 87 O "O5'" . DA A 1 5 ? 7.300 11.064 7.831 1.00 10.58 ? 5 DA A "O5'" 1
ATOM 88 C "C5'" . DA A 1 5 ? 8.232 10.037 7.561 1.00 9.42 ? 5 DA A "C5'" 1
ATOM 89 C "C4'" . DA A 1 5 ? 7.663 9.179 6.454 1.00 8.89 ? 5 DA A "C4'" 1
ATOM 90 O "O4'" . DA A 1 5 ? 7.494 9.980 5.260 1.00 9.25 ? 5 DA A "O4'" 1
ATOM 91 C "C3'" . DA A 1 5 ? 8.567 8.027 6.051 1.00 8.70 ? 5 DA A "C3'" 1
ATOM 92 O "O3'" . DA A 1 5 ? 8.258 6.898 6.857 1.00 9.21 ? 5 DA A "O3'" 1
ATOM 93 C "C2'" . DA A 1 5 ? 8.217 7.825 4.583 1.00 8.73 ? 5 DA A "C2'" 1
ATOM 94 C "C1'" . DA A 1 5 ? 8.042 9.277 4.161 1.00 8.73 ? 5 DA A "C1'" 1
ATOM 95 N N9 . DA A 1 5 ? 9.263 9.959 3.708 1.00 8.22 ? 5 DA A N9 1
ATOM 96 C C8 . DA A 1 5 ? 9.875 11.049 4.274 1.00 8.71 ? 5 DA A C8 1
ATOM 97 N N7 . DA A 1 5 ? 10.937 11.460 3.624 1.00 9.13 ? 5 DA A N7 1
ATOM 98 C C5 . DA A 1 5 ? 11.027 10.585 2.554 1.00 7.90 ? 5 DA A C5 1
ATOM 99 C C6 . DA A 1 5 ? 11.938 10.480 1.484 1.00 7.92 ? 5 DA A C6 1
ATOM 100 N N6 . DA A 1 5 ? 12.973 11.311 1.306 1.00 8.61 ? 5 DA A N6 1
ATOM 101 N N1 . DA A 1 5 ? 11.733 9.499 0.584 1.00 7.52 ? 5 DA A N1 1
ATOM 102 C C2 . DA A 1 5 ? 10.711 8.657 0.733 1.00 8.28 ? 5 DA A C2 1
ATOM 103 N N3 . DA A 1 5 ? 9.792 8.658 1.701 1.00 7.90 ? 5 DA A N3 1
ATOM 104 C C4 . DA A 1 5 ? 10.004 9.651 2.583 1.00 7.96 ? 5 DA A C4 1
ATOM 105 P P . DC A 1 6 ? 9.412 5.900 7.328 1.00 10.23 ? 6 DC A P 1
ATOM 106 O OP1 . DC A 1 6 ? 8.766 4.880 8.178 1.00 11.29 ? 6 DC A OP1 1
ATOM 107 O OP2 . DC A 1 6 ? 10.534 6.699 7.855 1.00 10.78 ? 6 DC A OP2 1
ATOM 108 O "O5'" . DC A 1 6 ? 9.923 5.274 5.956 1.00 9.75 ? 6 DC A "O5'" 1
ATOM 109 C "C5'" . DC A 1 6 ? 9.094 4.352 5.258 1.00 10.11 ? 6 DC A "C5'" 1
ATOM 110 C "C4'" . DC A 1 6 ? 9.720 3.968 3.938 1.00 9.76 ? 6 DC A "C4'" 1
ATOM 111 O "O4'" . DC A 1 6 ? 9.938 5.141 3.125 1.00 9.73 ? 6 DC A "O4'" 1
ATOM 112 C "C3'" . DC A 1 6 ? 11.110 3.378 4.089 1.00 10.34 ? 6 DC A "C3'" 1
ATOM 113 O "O3'" . DC A 1 6 ? 11.026 2.022 4.503 1.00 11.15 ? 6 DC A "O3'" 1
ATOM 114 C "C2'" . DC A 1 6 ? 11.655 3.565 2.681 1.00 9.75 ? 6 DC A "C2'" 1
ATOM 115 C "C1'" . DC A 1 6 ? 11.132 4.962 2.375 1.00 9.17 ? 6 DC A "C1'" 1
ATOM 116 N N1 . DC A 1 6 ? 12.078 6.084 2.668 1.00 8.05 ? 6 DC A N1 1
ATOM 117 C C2 . DC A 1 6 ? 13.123 6.316 1.765 1.00 8.18 ? 6 DC A C2 1
ATOM 118 O O2 . DC A 1 6 ? 13.237 5.578 0.778 1.00 9.48 ? 6 DC A O2 1
ATOM 119 N N3 . DC A 1 6 ? 13.970 7.343 2.003 1.00 7.28 ? 6 DC A N3 1
ATOM 120 C C4 . DC A 1 6 ? 13.835 8.122 3.079 1.00 7.78 ? 6 DC A C4 1
ATOM 121 N N4 . DC A 1 6 ? 14.715 9.115 3.238 1.00 8.60 ? 6 DC A N4 1
ATOM 122 C C5 . DC A 1 6 ? 12.781 7.904 4.020 1.00 7.72 ? 6 DC A C5 1
ATOM 123 C C6 . DC A 1 6 ? 11.938 6.887 3.773 1.00 7.84 ? 6 DC A C6 1
ATOM 124 P P . DA A 1 7 ? 12.230 1.349 5.311 1.00 12.31 ? 7 DA A P 1
ATOM 125 O OP1 . DA A 1 7 ? 11.742 0.037 5.792 1.00 13.38 ? 7 DA A OP1 1
ATOM 126 O OP2 . DA A 1 7 ? 12.844 2.315 6.253 1.00 12.16 ? 7 DA A OP2 1
ATOM 127 O "O5'" . DA A 1 7 ? 13.303 1.109 4.159 1.00 10.70 ? 7 DA A "O5'" 1
ATOM 128 C "C5'" . DA A 1 7 ? 13.062 0.171 3.115 1.00 10.46 ? 7 DA A "C5'" 1
ATOM 129 C "C4'" . DA A 1 7 ? 14.258 0.183 2.185 1.00 9.22 ? 7 DA A "C4'" 1
ATOM 130 O "O4'" . DA A 1 7 ? 14.417 1.504 1.624 1.00 9.31 ? 7 DA A "O4'" 1
ATOM 131 C "C3'" . DA A 1 7 ? 15.589 -0.091 2.868 1.00 8.99 ? 7 DA A "C3'" 1
ATOM 132 O "O3'" . DA A 1 7 ? 15.796 -1.485 2.943 1.00 9.74 ? 7 DA A "O3'" 1
ATOM 133 C "C2'" . DA A 1 7 ? 16.595 0.584 1.944 1.00 9.24 ? 7 DA A "C2'" 1
ATOM 134 C "C1'" . DA A 1 7 ? 15.796 1.777 1.467 1.00 8.55 ? 7 DA A "C1'" 1
ATOM 135 N N9 . DA A 1 7 ? 16.030 3.046 2.142 1.00 7.71 ? 7 DA A N9 1
ATOM 136 C C8 . DA A 1 7 ? 15.297 3.582 3.169 1.00 7.86 ? 7 DA A C8 1
ATOM 137 N N7 . DA A 1 7 ? 15.713 4.767 3.538 1.00 7.37 ? 7 DA A N7 1
ATOM 138 C C5 . DA A 1 7 ? 16.781 5.027 2.688 1.00 7.47 ? 7 DA A C5 1
ATOM 139 C C6 . DA A 1 7 ? 17.660 6.125 2.550 1.00 8.13 ? 7 DA A C6 1
ATOM 140 N N6 . DA A 1 7 ? 17.593 7.230 3.300 1.00 7.62 ? 7 DA A N6 1
ATOM 141 N N1 . DA A 1 7 ? 18.616 6.049 1.593 1.00 7.62 ? 7 DA A N1 1
ATOM 142 C C2 . DA A 1 7 ? 18.701 4.955 0.826 1.00 7.79 ? 7 DA A C2 1
ATOM 143 N N3 . DA A 1 7 ? 17.928 3.868 0.861 1.00 7.86 ? 7 DA A N3 1
ATOM 144 C C4 . DA A 1 7 ? 16.984 3.972 1.816 1.00 8.11 ? 7 DA A C4 1
ATOM 145 P P . DC A 1 8 ? 16.722 -2.122 4.079 1.00 10.96 ? 8 DC A P 1
ATOM 146 O OP1 . DC A 1 8 ? 16.602 -3.587 3.918 1.00 11.18 ? 8 DC A OP1 1
ATOM 147 O OP2 . DC A 1 8 ? 16.398 -1.508 5.383 1.00 11.98 ? 8 DC A OP2 1
ATOM 148 O "O5'" . DC A 1 8 ? 18.196 -1.658 3.682 1.00 10.14 ? 8 DC A "O5'" 1
ATOM 149 C "C5'" . DC A 1 8 ? 18.803 -2.170 2.503 1.00 9.32 ? 8 DC A "C5'" 1
ATOM 150 C "C4'" . DC A 1 8 ? 20.141 -1.500 2.275 1.00 9.66 ? 8 DC A "C4'" 1
ATOM 151 O "O4'" . DC A 1 8 ? 19.933 -0.067 2.250 1.00 9.29 ? 8 DC A "O4'" 1
ATOM 152 C "C3'" . DC A 1 8 ? 21.183 -1.789 3.350 1.00 10.22 ? 8 DC A "C3'" 1
ATOM 153 O "O3'" . DC A 1 8 ? 22.414 -2.141 2.732 1.00 12.65 ? 8 DC A "O3'" 1
ATOM 154 C "C2'" . DC A 1 8 ? 21.320 -0.471 4.104 1.00 9.92 ? 8 DC A "C2'" 1
ATOM 155 C "C1'" . DC A 1 8 ? 20.907 0.555 3.050 1.00 8.87 ? 8 DC A "C1'" 1
ATOM 156 N N1 . DC A 1 8 ? 20.318 1.781 3.656 1.00 8.33 ? 8 DC A N1 1
ATOM 157 C C2 . DC A 1 8 ? 20.901 3.036 3.415 1.00 8.87 ? 8 DC A C2 1
ATOM 158 O O2 . DC A 1 8 ? 21.889 3.114 2.678 1.00 8.33 ? 8 DC A O2 1
ATOM 159 N N3 . DC A 1 8 ? 20.357 4.127 4.009 1.00 8.09 ? 8 DC A N3 1
ATOM 160 C C4 . DC A 1 8 ? 19.288 4.015 4.807 1.00 7.84 ? 8 DC A C4 1
ATOM 161 N N4 . DC A 1 8 ? 18.803 5.127 5.367 1.00 7.87 ? 8 DC A N4 1
ATOM 162 C C5 . DC A 1 8 ? 18.666 2.750 5.056 1.00 7.88 ? 8 DC A C5 1
ATOM 163 C C6 . DC A 1 8 ? 19.217 1.677 4.469 1.00 9.06 ? 8 DC A C6 1
HETATM 164 O O . HOH B 2 . ? 16.433 26.943 -0.762 1.00 19.23 ? 9 HOH A O 1
HETATM 165 O O . HOH B 2 . ? 2.994 20.318 2.044 1.00 16.13 ? 10 HOH A O 1
HETATM 166 O O . HOH B 2 . ? 7.398 7.108 1.350 1.00 12.74 ? 11 HOH A O 1
HETATM 167 O O . HOH B 2 . ? 7.410 2.337 1.866 1.00 21.33 ? 12 HOH A O 1
HETATM 168 O O . HOH B 2 . ? 3.550 17.583 5.895 1.00 21.12 ? 13 HOH A O 1
HETATM 169 O O . HOH B 2 . ? 21.246 -4.461 1.138 1.00 19.79 ? 14 HOH A O 1
HETATM 170 O O . HOH B 2 . ? 4.109 19.389 7.820 1.00 21.88 ? 15 HOH A O 1
HETATM 171 O O . HOH B 2 . ? 13.127 21.694 0.694 1.00 25.72 ? 16 HOH A O 1
HETATM 172 O O . HOH B 2 . ? 11.508 20.357 -6.564 1.00 31.16 ? 17 HOH A O 1
HETATM 173 O O . HOH B 2 . ? 24.078 -0.049 1.483 1.00 21.16 ? 18 HOH A O 1
HETATM 174 O O . HOH B 2 . ? 15.519 2.452 7.082 1.00 22.71 ? 19 HOH A O 1
HETATM 175 O O . HOH B 2 . ? 12.369 19.255 -0.169 1.00 24.71 ? 20 HOH A O 1
HETATM 176 O O . HOH B 2 . ? 14.437 10.963 5.509 1.00 24.79 ? 21 HOH A O 1
HETATM 177 O O . HOH B 2 . ? 14.730 22.991 -3.448 1.00 27.15 ? 22 HOH A O 1
HETATM 178 O O . HOH B 2 . ? 6.266 3.759 7.277 1.00 26.89 ? 23 HOH A O 1
HETATM 179 O O . HOH B 2 . ? 3.772 4.397 1.282 1.00 34.93 ? 24 HOH A O 1
HETATM 180 O O . HOH B 2 . ? 9.002 18.544 -6.272 1.00 25.64 ? 25 HOH A O 1
HETATM 181 O O . HOH B 2 . ? 10.559 13.771 6.493 1.00 35.57 ? 26 HOH A O 1
HETATM 182 O O . HOH B 2 . ? 11.700 17.623 -2.351 1.00 31.19 ? 27 HOH A O 1
HETATM 183 O O . HOH B 2 . ? 11.706 9.392 7.108 1.00 32.13 ? 28 HOH A O 1
HETATM 184 O O . HOH B 2 . ? 13.150 7.111 7.459 1.00 33.11 ? 29 HOH A O 1
HETATM 185 O O . HOH B 2 . ? 16.087 7.632 5.966 1.00 23.69 ? 30 HOH A O 1
HETATM 186 O O . HOH B 2 . ? 14.250 5.196 5.827 1.00 27.71 ? 31 HOH A O 1
HETATM 187 O O . HOH B 2 . ? 19.124 1.377 -0.161 1.00 14.27 ? 32 HOH A O 1
HETATM 188 O O . HOH B 2 . ? 16.759 -4.811 1.543 1.00 15.27 ? 33 HOH A O 1
HETATM 189 O O . HOH B 2 . ? 3.886 22.173 -0.002 1.00 15.79 ? 34 HOH A O 1
HETATM 190 O O . HOH B 2 . ? 13.496 15.875 1.158 1.00 36.21 ? 35 HOH A O 1
HETATM 191 O O . HOH B 2 . ? 6.368 4.831 2.572 1.00 16.80 ? 36 HOH A O 1
HETATM 192 O O . HOH B 2 . ? 4.273 17.903 3.204 1.00 19.94 ? 37 HOH A O 1
HETATM 193 O O . HOH B 2 . ? 14.462 26.535 2.802 1.00 28.28 ? 38 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 T5O 4 4 4 T5O T5O 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 HOH 1 9 9 HOH HOH A .
B 2 HOH 2 10 10 HOH HOH A .
B 2 HOH 3 11 1 HOH HOH A .
B 2 HOH 4 12 12 HOH HOH A .
B 2 HOH 5 13 13 HOH HOH A .
B 2 HOH 6 14 14 HOH HOH A .
B 2 HOH 7 15 15 HOH HOH A .
B 2 HOH 8 16 16 HOH HOH A .
B 2 HOH 9 17 17 HOH HOH A .
B 2 HOH 10 18 18 HOH HOH A .
B 2 HOH 11 19 19 HOH HOH A .
B 2 HOH 12 20 20 HOH HOH A .
B 2 HOH 13 21 21 HOH HOH A .
B 2 HOH 14 22 22 HOH HOH A .
B 2 HOH 15 23 23 HOH HOH A .
B 2 HOH 16 24 24 HOH HOH A .
B 2 HOH 17 25 25 HOH HOH A .
B 2 HOH 18 26 26 HOH HOH A .
B 2 HOH 19 27 27 HOH HOH A .
B 2 HOH 20 28 28 HOH HOH A .
B 2 HOH 21 29 29 HOH HOH A .
B 2 HOH 22 30 30 HOH HOH A .
B 2 HOH 23 31 31 HOH HOH A .
B 2 HOH 24 32 2 HOH HOH A .
B 2 HOH 25 33 3 HOH HOH A .
B 2 HOH 26 34 4 HOH HOH A .
B 2 HOH 27 35 5 HOH HOH A .
B 2 HOH 28 36 6 HOH HOH A .
B 2 HOH 29 37 7 HOH HOH A .
B 2 HOH 30 38 8 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 T5O 4 A T5O 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
#
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)' 1940 ?
1 MORE 8 ?
1 'SSA (A^2)' 2910 ?
#
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_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 2009-10-06
2 'Structure model' 1 1 2011-07-13
3 'Structure model' 1 2 2023-08-02
4 'Structure model' 1 3 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 3 'Structure model' 'Derived calculations'
5 3 'Structure model' 'Source and taxonomy'
6 4 'Structure model' 'Data collection'
7 4 '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 3 'Structure model' citation
2 3 'Structure model' citation_author
3 3 'Structure model' database_2
4 3 'Structure model' pdbx_entity_src_syn
5 3 'Structure model' struct_conn
6 4 'Structure model' chem_comp_atom
7 4 'Structure model' chem_comp_bond
8 4 'Structure model' pdbx_initial_refinement_model
#
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 3 'Structure model' '_citation.country'
2 3 'Structure model' '_citation.journal_abbrev'
3 3 'Structure model' '_citation.journal_id_CSD'
4 3 'Structure model' '_citation.journal_id_ISSN'
5 3 'Structure model' '_citation.journal_volume'
6 3 'Structure model' '_citation.pdbx_database_id_DOI'
7 3 'Structure model' '_citation.title'
8 3 'Structure model' '_citation.year'
9 3 'Structure model' '_citation_author.name'
10 3 'Structure model' '_database_2.pdbx_DOI'
11 3 'Structure model' '_database_2.pdbx_database_accession'
12 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag'
#
_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 11.4162
_pdbx_refine_tls.origin_y 12.7391
_pdbx_refine_tls.origin_z 2.3922
_pdbx_refine_tls.T[1][1] 0.0418
_pdbx_refine_tls.T[2][2] 0.0201
_pdbx_refine_tls.T[3][3] 0.0250
_pdbx_refine_tls.T[1][2] 0.0001
_pdbx_refine_tls.T[1][3] -0.0099
_pdbx_refine_tls.T[2][3] -0.0003
_pdbx_refine_tls.L[1][1] 0.7644
_pdbx_refine_tls.L[2][2] 2.6011
_pdbx_refine_tls.L[3][3] 0.1056
_pdbx_refine_tls.L[1][2] -0.9107
_pdbx_refine_tls.L[1][3] -0.0164
_pdbx_refine_tls.L[2][3] -0.3799
_pdbx_refine_tls.S[1][1] -0.0447
_pdbx_refine_tls.S[1][2] -0.0140
_pdbx_refine_tls.S[1][3] -0.0434
_pdbx_refine_tls.S[2][1] 0.2121
_pdbx_refine_tls.S[2][2] 0.0378
_pdbx_refine_tls.S[2][3] -0.0153
_pdbx_refine_tls.S[3][1] 0.0030
_pdbx_refine_tls.S[3][2] 0.0553
_pdbx_refine_tls.S[3][3] 0.0068
#
_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
SHELXS phasing . ? 2
REFMAC refinement 5.0 ? 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 DG
_pdbx_validate_rmsd_angle.auth_seq_id_1 3
_pdbx_validate_rmsd_angle.PDB_ins_code_1 ?
_pdbx_validate_rmsd_angle.label_alt_id_1 ?
_pdbx_validate_rmsd_angle.auth_atom_id_2 "C4'"
_pdbx_validate_rmsd_angle.auth_asym_id_2 A
_pdbx_validate_rmsd_angle.auth_comp_id_2 DG
_pdbx_validate_rmsd_angle.auth_seq_id_2 3
_pdbx_validate_rmsd_angle.PDB_ins_code_2 ?
_pdbx_validate_rmsd_angle.label_alt_id_2 ?
_pdbx_validate_rmsd_angle.auth_atom_id_3 "C3'"
_pdbx_validate_rmsd_angle.auth_asym_id_3 A
_pdbx_validate_rmsd_angle.auth_comp_id_3 DG
_pdbx_validate_rmsd_angle.auth_seq_id_3 3
_pdbx_validate_rmsd_angle.PDB_ins_code_3 ?
_pdbx_validate_rmsd_angle.label_alt_id_3 ?
_pdbx_validate_rmsd_angle.angle_value 101.67
_pdbx_validate_rmsd_angle.angle_target_value 104.50
_pdbx_validate_rmsd_angle.angle_deviation -2.83
_pdbx_validate_rmsd_angle.angle_standard_deviation 0.40
_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
T5O P P N N 111
T5O N1 N N N 112
T5O C2 C N N 113
T5O O2 O N N 114
T5O N3 N N N 115
T5O C4 C N N 116
T5O O4 O N N 117
T5O C5 C N N 118
T5O O5 O N N 119
T5O C6 C N N 120
T5O "C1'" C N R 121
T5O OP3 O N N 122
T5O "C2'" C N N 123
T5O OP2 O N N 124
T5O "C3'" C N S 125
T5O "O3'" O N N 126
T5O "C4'" C N R 127
T5O "O4'" O N N 128
T5O "C5'" C N N 129
T5O "O5'" O N N 130
T5O C7 C N N 131
T5O H6 H N N 132
T5O "H1'" H N N 133
T5O HOP3 H N N 134
T5O "H2'" H N N 135
T5O "H2'A" H N N 136
T5O HOP2 H N N 137
T5O "H3'" H N N 138
T5O "HO3'" H N N 139
T5O "H4'" H N N 140
T5O "H5'" H N N 141
T5O "H5'A" H N N 142
T5O HC7 H N N 143
T5O HC7A H N N 144
T5O HC7B H N N 145
T5O HN3 H N N 146
T5O OP1 O N N 147
UMS OP3 O N N 148
UMS P P N N 149
UMS OP1 O N N 150
UMS OP2 O N N 151
UMS "O5'" O N N 152
UMS "C5'" C N N 153
UMS "C4'" C N R 154
UMS "O4'" O N N 155
UMS "C3'" C N R 156
UMS "O3'" O N N 157
UMS "C2'" C N R 158
UMS "SE2'" SE N N 159
UMS "C1'" C N R 160
UMS "CA'" C N N 161
UMS N1 N N N 162
UMS C2 C N N 163
UMS O2 O N N 164
UMS N3 N N N 165
UMS C4 C N N 166
UMS O4 O N N 167
UMS C5 C N N 168
UMS C6 C N N 169
UMS HOP3 H N N 170
UMS HOP2 H N N 171
UMS "H5'" H N N 172
UMS "H5'2" H N N 173
UMS "H4'" H N N 174
UMS "H3'" H N N 175
UMS "HO3'" H N N 176
UMS "H2'" H N N 177
UMS "H1'" H N N 178
UMS "HA'" H N N 179
UMS "HA'2" H N N 180
UMS "HA'3" H N N 181
UMS H3 H N N 182
UMS H5 H N N 183
UMS H6 H N N 184
#
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
T5O P OP3 sing N N 115
T5O N1 C6 sing N N 116
T5O N1 "C1'" sing N N 117
T5O C2 N1 sing N N 118
T5O O2 C2 doub N N 119
T5O N3 C2 sing N N 120
T5O N3 C4 sing N N 121
T5O N3 HN3 sing N N 122
T5O C4 C5 sing N N 123
T5O O4 C4 doub N N 124
T5O C5 O5 sing N N 125
T5O C5 C6 doub N N 126
T5O O5 C7 sing N N 127
T5O C6 H6 sing N N 128
T5O "C1'" "O4'" sing N N 129
T5O "C1'" "C2'" sing N N 130
T5O "C1'" "H1'" sing N N 131
T5O OP3 HOP3 sing N N 132
T5O "C2'" "C3'" sing N N 133
T5O "C2'" "H2'" sing N N 134
T5O "C2'" "H2'A" sing N N 135
T5O OP2 P sing N N 136
T5O OP2 HOP2 sing N N 137
T5O "C3'" "O3'" sing N N 138
T5O "C3'" "H3'" sing N N 139
T5O "O3'" "HO3'" sing N N 140
T5O "C4'" "C3'" sing N N 141
T5O "C4'" "C5'" sing N N 142
T5O "C4'" "H4'" sing N N 143
T5O "O4'" "C4'" sing N N 144
T5O "C5'" "H5'" sing N N 145
T5O "C5'" "H5'A" sing N N 146
T5O "O5'" P sing N N 147
T5O "O5'" "C5'" sing N N 148
T5O C7 HC7 sing N N 149
T5O C7 HC7A sing N N 150
T5O C7 HC7B sing N N 151
T5O P OP1 doub N N 152
UMS OP3 P sing N N 153
UMS OP3 HOP3 sing N N 154
UMS P OP1 doub N N 155
UMS P OP2 sing N N 156
UMS P "O5'" sing N N 157
UMS OP2 HOP2 sing N N 158
UMS "O5'" "C5'" sing N N 159
UMS "C5'" "C4'" sing N N 160
UMS "C5'" "H5'" sing N N 161
UMS "C5'" "H5'2" sing N N 162
UMS "C4'" "O4'" sing N N 163
UMS "C4'" "C3'" sing N N 164
UMS "C4'" "H4'" sing N N 165
UMS "O4'" "C1'" sing N N 166
UMS "C3'" "O3'" sing N N 167
UMS "C3'" "C2'" sing N N 168
UMS "C3'" "H3'" sing N N 169
UMS "O3'" "HO3'" sing N N 170
UMS "C2'" "SE2'" sing N N 171
UMS "C2'" "C1'" sing N N 172
UMS "C2'" "H2'" sing N N 173
UMS "SE2'" "CA'" sing N N 174
UMS "C1'" N1 sing N N 175
UMS "C1'" "H1'" sing N N 176
UMS "CA'" "HA'" sing N N 177
UMS "CA'" "HA'2" sing N N 178
UMS "CA'" "HA'3" sing N N 179
UMS N1 C2 sing N N 180
UMS N1 C6 sing N N 181
UMS C2 O2 doub N N 182
UMS C2 N3 sing N N 183
UMS N3 C4 sing N N 184
UMS N3 H3 sing N N 185
UMS C4 O4 doub N N 186
UMS C4 C5 sing N N 187
UMS C5 C6 doub N N 188
UMS C5 H5 sing N N 189
UMS C6 H6 sing N N 190
#
_ndb_struct_conf_na.entry_id 3IJK
_ndb_struct_conf_na.feature 'a-form double helix'
#
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 -0.292 -0.106 -0.351 -19.637 -12.590 -1.703 1 A_DG1:DC8_A A 1 ? A 8 ? 19 1
1 A UMS 2 1_555 A DA 7 7_555 -0.009 -0.080 0.237 -9.281 -10.807 1.992 2 A_UMS2:DA7_A A 2 ? A 7 ? 20 1
1 A DG 3 1_555 A DC 6 7_555 -0.250 -0.160 0.270 -5.641 -13.698 0.673 3 A_DG3:DC6_A A 3 ? A 6 ? 19 1
1 A T5O 4 1_555 A DA 5 7_555 -0.194 -0.156 0.335 -5.432 -10.865 -4.584 4 A_T5O4:DA5_A A 4 ? A 5 ? 20 1
1 A DA 5 1_555 A T5O 4 7_555 0.194 -0.156 0.335 5.432 -10.865 -4.584 5 A_DA5:T5O4_A A 5 ? A 4 ? 20 1
1 A DC 6 1_555 A DG 3 7_555 0.250 -0.160 0.270 5.641 -13.698 0.673 6 A_DC6:DG3_A A 6 ? A 3 ? 19 1
1 A DA 7 1_555 A UMS 2 7_555 0.009 -0.080 0.237 9.281 -10.808 1.992 7 A_DA7:UMS2_A A 7 ? A 2 ? 20 1
1 A DC 8 1_555 A DG 1 7_555 0.292 -0.106 -0.351 19.637 -12.591 -1.703 8 A_DC8:DG1_A A 8 ? A 1 ? 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 0.352 -0.902 3.130 -3.736 11.150 31.039 -3.284 -1.186 2.602 19.959
6.687 33.141 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 0.743 -1.447 3.009 1.451 10.112 29.910 -4.266 -1.136 2.435 18.910
-2.713 31.569 2 AA_UMS2DG3:DC6DA7_AA A 2 ? A 7 ? A 3 ? A 6 ?
1 A DG 3 1_555 A DC 6 7_555 A T5O 4 1_555 A DA 5 7_555 -0.061 -2.101 3.303 1.919 -0.632 33.123 -3.571 0.434 3.333 -1.107
-3.362 33.183 3 AA_DG3T5O4:DA5DC6_AA A 3 ? A 6 ? A 4 ? A 5 ?
1 A T5O 4 1_555 A DA 5 7_555 A DA 5 1_555 A T5O 4 7_555 0.000 -1.654 2.901 0.000 6.313 28.601 -4.411 0.000 2.486 12.586
0.000 29.275 4 AA_T5O4DA5:T5O4DA5_AA A 4 ? A 5 ? A 5 ? A 4 ?
1 A DA 5 1_555 A T5O 4 7_555 A DC 6 1_555 A DG 3 7_555 0.061 -2.101 3.303 -1.919 -0.632 33.123 -3.571 -0.434 3.333 -1.107
3.362 33.183 5 AA_DA5DC6:DG3T5O4_AA A 5 ? A 4 ? A 6 ? A 3 ?
1 A DC 6 1_555 A DG 3 7_555 A DA 7 1_555 A UMS 2 7_555 -0.743 -1.447 3.009 -1.451 10.112 29.910 -4.266 1.136 2.435 18.911
2.713 31.569 6 AA_DC6DA7:UMS2DG3_AA A 6 ? A 3 ? A 7 ? A 2 ?
1 A DA 7 1_555 A UMS 2 7_555 A DC 8 1_555 A DG 1 7_555 -0.352 -0.902 3.130 3.736 11.150 31.039 -3.284 1.186 2.602 19.959
-6.687 33.141 7 AA_DA7DC8:DG1UMS2_AA A 7 ? A 2 ? A 8 ? A 1 ?
#
_pdbx_entity_nonpoly.entity_id 2
_pdbx_entity_nonpoly.name water
_pdbx_entity_nonpoly.comp_id 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 ?
#