HEADER DNA 05-AUG-09 3IKI
TITLE 5-SME-DU CONTAINING DNA OCTAMER
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SYNTHESIZED BY SOLID PHASE SYNTHESIS
KEYWDS SELENIUM, NUCLEIC ACID, 5-SME-DEOXYURIDINE, 2'-SEME-DEOXYURIDINE, DNA
EXPDTA X-RAY DIFFRACTION
AUTHOR J.SHENG,A.E.A.HASSAN,W.ZHANG,J.GAN,Z.HUANG
REVDAT 5 06-SEP-23 3IKI 1 REMARK LINK
REVDAT 4 26-SEP-12 3IKI 1 JRNL
REVDAT 3 13-JUN-12 3IKI 1 JRNL
REVDAT 2 13-JUL-11 3IKI 1 VERSN
REVDAT 1 09-MAR-10 3IKI 0
JRNL AUTH J.SHENG,W.ZHANG,A.E.HASSAN,J.GAN,A.S.SOARES,S.GENG,Y.REN,
JRNL AUTH 2 Z.HUANG
JRNL TITL HYDROGEN BOND FORMATION BETWEEN THE NATURALLY MODIFIED
JRNL TITL 2 NUCLEOBASE AND PHOSPHATE BACKBONE.
JRNL REF NUCLEIC ACIDS RES. V. 40 8111 2012
JRNL REFN ISSN 0305-1048
JRNL PMID 22641848
JRNL DOI 10.1093/NAR/GKS426
REMARK 2
REMARK 2 RESOLUTION. 1.38 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.32
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0
REMARK 3 NUMBER OF REFLECTIONS : 4373
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.178
REMARK 3 FREE R VALUE : 0.194
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700
REMARK 3 FREE R VALUE TEST SET COUNT : 216
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.38
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.42
REMARK 3 REFLECTION IN BIN (WORKING SET) : 216
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.53
REMARK 3 BIN R VALUE (WORKING SET) : 0.2030
REMARK 3 BIN FREE R VALUE SET COUNT : 14
REMARK 3 BIN FREE R VALUE : 0.1570
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 0
REMARK 3 NUCLEIC ACID ATOMS : 163
REMARK 3 HETEROGEN ATOMS : 1
REMARK 3 SOLVENT ATOMS : 38
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.13
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.12000
REMARK 3 B22 (A**2) : 0.12000
REMARK 3 B33 (A**2) : -0.24000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.061
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.592
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 180 ; 0.007 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 270 ; 1.467 ; 3.000
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 31 ; 0.057 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 83 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 66 ; 0.371 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 103 ; 0.277 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 29 ; 0.102 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 26 ; 0.180 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.083 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 261 ; 0.825 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 270 ; 1.249 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 1 A 8
REMARK 3 ORIGIN FOR THE GROUP (A): 31.5133 30.4882 2.3842
REMARK 3 T TENSOR
REMARK 3 T11: 0.0169 T22: -0.0057
REMARK 3 T33: 0.0077 T12: -0.0065
REMARK 3 T13: 0.0054 T23: -0.0025
REMARK 3 L TENSOR
REMARK 3 L11: 0.1824 L22: 1.3050
REMARK 3 L33: 0.2928 L12: -0.3805
REMARK 3 L13: -0.0034 L23: 0.2072
REMARK 3 S TENSOR
REMARK 3 S11: -0.0049 S12: 0.0122 S13: 0.0094
REMARK 3 S21: 0.1295 S22: 0.0189 S23: -0.0139
REMARK 3 S31: 0.0248 S32: -0.0403 S33: -0.0140
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3IKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-09.
REMARK 100 THE DEPOSITION ID IS D_1000054525.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-OCT-08
REMARK 200 TEMPERATURE (KELVIN) : 99
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X12B
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795
REMARK 200 MONOCHROMATOR : CHANNEL-CUT SI(111)
REMARK 200 MONOCHROMATOR
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4616
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0
REMARK 200 DATA REDUNDANCY : 8.400
REMARK 200 R MERGE (I) : 0.05700
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 23.0200
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43
REMARK 200 COMPLETENESS FOR SHELL (%) : 67.8
REMARK 200 DATA REDUNDANCY IN SHELL : 5.20
REMARK 200 R MERGE FOR SHELL (I) : 0.24500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 5.860
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASES
REMARK 200 STARTING MODEL: 1DNS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.67
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V / V MPD, 40 MM NA CACODYLATE PH
REMARK 280 7.0, 12 MM SPERMINE TETRA-HCL, 40 MM LITHIUM CHLORIDE, 80 MM
REMARK 280 STRONTIUM CHLORIDE / 20 MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 11.84350
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.44100
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.44100
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.76525
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.44100
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.44100
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 5.92175
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.44100
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.44100
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.76525
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.44100
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.44100
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 5.92175
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 11.84350
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2240 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 2810 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 11 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DG A 3 OP2
REMARK 620 2 HOH A 36 O 130.6
REMARK 620 3 HOH A 45 O 99.3 102.8
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 11
DBREF 3IKI A 1 8 PDB 3IKI 3IKI 1 8
SEQRES 1 A 8 DG UMS DG US2 DA DC DA DC
MODRES 3IKI UMS A 2 DU
MODRES 3IKI US2 A 4 DU
HET UMS A 2 21
HET US2 A 4 21
HET MG A 11 1
HETNAM UMS 2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE
HETNAM US2 2'-DEOXY-5-(METHYLSULFANYL)URIDINE 5'-(DIHYDROGEN
HETNAM 2 US2 PHOSPHATE)
HETNAM MG MAGNESIUM ION
HETSYN US2 5-SME-DEOXYURIDINE-5'-PHOSPHATE
FORMUL 1 UMS C10 H15 N2 O8 P SE
FORMUL 1 US2 C10 H15 N2 O8 P S
FORMUL 2 MG MG 2+
FORMUL 3 HOH *38(H2 O)
LINK O3' DG A 1 P UMS A 2 1555 1555 1.60
LINK O3' UMS A 2 P DG A 3 1555 1555 1.60
LINK O3' DG A 3 P US2 A 4 1555 1555 1.60
LINK O3' US2 A 4 P DA A 5 1555 1555 1.60
LINK OP2 DG A 3 MG MG A 11 1555 1555 2.12
LINK MG MG A 11 O HOH A 36 1555 1555 2.61
LINK MG MG A 11 O HOH A 45 1555 1555 2.68
SITE 1 AC1 4 UMS A 2 DG A 3 HOH A 36 HOH A 45
CRYST1 42.882 42.882 23.687 90.00 90.00 90.00 P 43 21 2 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.023320 0.000000 0.000000 0.00000
SCALE2 0.000000 0.023320 0.000000 0.00000
SCALE3 0.000000 0.000000 0.042217 0.00000
ATOM 1 O5' DG A 1 29.200 19.006 -5.269 1.00 10.16 O
ATOM 2 C5' DG A 1 29.102 17.599 -5.012 1.00 8.50 C
ATOM 3 C4' DG A 1 30.337 17.073 -4.294 1.00 8.52 C
ATOM 4 O4' DG A 1 31.516 17.253 -5.121 1.00 8.26 O
ATOM 5 C3' DG A 1 30.689 17.780 -2.994 1.00 8.15 C
ATOM 6 O3' DG A 1 29.917 17.237 -1.924 1.00 8.52 O
ATOM 7 C2' DG A 1 32.172 17.447 -2.873 1.00 8.35 C
ATOM 8 C1' DG A 1 32.630 17.593 -4.320 1.00 8.79 C
ATOM 9 N9 DG A 1 33.046 18.962 -4.621 1.00 8.63 N
ATOM 10 C8 DG A 1 32.299 19.947 -5.227 1.00 9.29 C
ATOM 11 N7 DG A 1 32.930 21.082 -5.340 1.00 9.41 N
ATOM 12 C5 DG A 1 34.171 20.842 -4.765 1.00 8.80 C
ATOM 13 C6 DG A 1 35.285 21.702 -4.603 1.00 8.54 C
ATOM 14 O6 DG A 1 35.392 22.885 -4.953 1.00 9.84 O
ATOM 15 N1 DG A 1 36.351 21.070 -3.970 1.00 9.08 N
ATOM 16 C2 DG A 1 36.342 19.757 -3.553 1.00 9.48 C
ATOM 17 N2 DG A 1 37.462 19.309 -2.967 1.00 10.47 N
ATOM 18 N3 DG A 1 35.307 18.934 -3.701 1.00 9.12 N
ATOM 19 C4 DG A 1 34.257 19.542 -4.310 1.00 8.79 C
HETATM 20 P UMS A 2 29.421 18.150 -0.706 1.00 9.05 P
HETATM 21 OP1 UMS A 2 28.566 17.307 0.151 1.00 10.34 O
HETATM 22 OP2 UMS A 2 28.924 19.445 -1.225 1.00 10.47 O
HETATM 23 O5' UMS A 2 30.757 18.496 0.103 1.00 8.89 O
HETATM 24 C5' UMS A 2 31.441 17.472 0.807 1.00 8.83 C
HETATM 25 C4' UMS A 2 32.791 17.955 1.276 1.00 9.12 C
HETATM 26 O4' UMS A 2 33.581 18.369 0.134 1.00 8.82 O
HETATM 27 C3' UMS A 2 32.756 19.173 2.179 1.00 10.51 C
HETATM 28 O3' UMS A 2 32.423 18.731 3.481 1.00 12.79 O
HETATM 29 C2' UMS A 2 34.192 19.676 2.028 1.00 9.97 C
HETATM 30 SE2' UMS A 2 35.473 18.592 3.062 0.80 11.05 SE
HETATM 31 C1' UMS A 2 34.417 19.438 0.533 1.00 8.91 C
HETATM 32 CA' UMS A 2 37.126 19.644 2.969 1.00 11.95 C
HETATM 33 N1 UMS A 2 34.107 20.625 -0.339 1.00 9.25 N
HETATM 34 C2 UMS A 2 35.086 21.588 -0.498 1.00 9.47 C
HETATM 35 O2 UMS A 2 36.173 21.525 0.045 1.00 10.23 O
HETATM 36 N3 UMS A 2 34.746 22.642 -1.310 1.00 9.45 N
HETATM 37 C4 UMS A 2 33.543 22.828 -1.974 1.00 9.06 C
HETATM 38 O4 UMS A 2 33.389 23.829 -2.666 1.00 9.46 O
HETATM 39 C5 UMS A 2 32.565 21.787 -1.765 1.00 9.55 C
HETATM 40 C6 UMS A 2 32.877 20.746 -0.974 1.00 9.05 C
ATOM 41 P DG A 3 31.679 19.652 4.556 1.00 15.71 P
ATOM 42 OP1 DG A 3 31.260 18.752 5.651 1.00 17.09 O
ATOM 43 OP2 DG A 3 30.721 20.539 3.869 1.00 16.48 O
ATOM 44 O5' DG A 3 32.908 20.543 5.059 1.00 15.23 O
ATOM 45 C5' DG A 3 32.843 21.945 5.006 1.00 13.73 C
ATOM 46 C4' DG A 3 34.257 22.474 4.941 1.00 13.22 C
ATOM 47 O4' DG A 3 34.749 22.336 3.591 1.00 12.36 O
ATOM 48 C3' DG A 3 34.357 23.950 5.234 1.00 12.39 C
ATOM 49 O3' DG A 3 34.459 24.186 6.669 1.00 9.15 O
ATOM 50 C2' DG A 3 35.586 24.360 4.437 1.00 11.58 C
ATOM 51 C1' DG A 3 35.429 23.505 3.188 1.00 10.43 C
ATOM 52 N9 DG A 3 34.648 24.135 2.126 1.00 10.22 N
ATOM 53 C8 DG A 3 33.428 23.744 1.627 1.00 9.97 C
ATOM 54 N7 DG A 3 32.986 24.510 0.667 1.00 9.92 N
ATOM 55 C5 DG A 3 33.985 25.467 0.517 1.00 9.40 C
ATOM 56 C6 DG A 3 34.076 26.571 -0.367 1.00 8.93 C
ATOM 57 O6 DG A 3 33.263 26.922 -1.229 1.00 9.41 O
ATOM 58 N1 DG A 3 35.255 27.297 -0.184 1.00 9.13 N
ATOM 59 C2 DG A 3 36.230 27.001 0.742 1.00 9.39 C
ATOM 60 N2 DG A 3 37.307 27.803 0.793 1.00 9.27 N
ATOM 61 N3 DG A 3 36.160 25.968 1.570 1.00 9.25 N
ATOM 62 C4 DG A 3 35.013 25.252 1.407 1.00 9.74 C
HETATM 63 P US2 A 4 34.000 25.547 7.366 1.00 9.16 P
HETATM 64 N1 US2 A 4 35.349 29.061 3.421 1.00 5.92 N
HETATM 65 C6 US2 A 4 34.393 28.074 3.644 1.00 5.69 C
HETATM 66 C2 US2 A 4 35.177 30.017 2.439 1.00 4.71 C
HETATM 67 O2 US2 A 4 35.968 30.918 2.207 1.00 4.70 O
HETATM 68 N3 US2 A 4 34.017 29.894 1.719 1.00 5.07 N
HETATM 69 C4 US2 A 4 33.024 28.938 1.884 1.00 5.05 C
HETATM 70 O4 US2 A 4 32.024 28.926 1.172 1.00 5.04 O
HETATM 71 C5 US2 A 4 33.257 27.957 2.936 1.00 5.87 C
HETATM 72 S5 US2 A 4 32.100 26.680 3.276 1.00 6.82 S
HETATM 73 C5A US2 A 4 30.857 27.447 4.289 1.00 9.62 C
HETATM 74 C1' US2 A 4 36.597 29.111 4.259 1.00 5.73 C
HETATM 75 O4' US2 A 4 36.828 27.841 4.861 1.00 7.43 O
HETATM 76 C4' US2 A 4 36.862 28.001 6.302 1.00 6.32 C
HETATM 77 C3' US2 A 4 36.066 29.277 6.546 1.00 5.74 C
HETATM 78 O3' US2 A 4 36.420 29.819 7.805 1.00 5.91 O
HETATM 79 C2' US2 A 4 36.527 30.143 5.380 1.00 6.02 C
HETATM 80 C5' US2 A 4 36.305 26.760 6.964 1.00 7.21 C
HETATM 81 O5' US2 A 4 34.908 26.665 6.673 1.00 7.56 O
HETATM 82 O1P US2 A 4 32.584 25.785 7.061 1.00 8.52 O
HETATM 83 O2P US2 A 4 34.409 25.429 8.789 1.00 11.42 O
ATOM 84 P DA A 5 35.464 30.875 8.528 1.00 6.43 P
ATOM 85 OP1 DA A 5 35.871 30.926 9.984 1.00 11.11 O
ATOM 86 OP2 DA A 5 34.015 30.623 8.221 1.00 11.96 O
ATOM 87 O5' DA A 5 35.911 32.253 7.849 1.00 8.28 O
ATOM 88 C5' DA A 5 35.012 33.322 7.615 1.00 8.06 C
ATOM 89 C4' DA A 5 35.548 34.164 6.476 1.00 7.41 C
ATOM 90 O4' DA A 5 35.696 33.336 5.293 1.00 7.13 O
ATOM 91 C3' DA A 5 34.652 35.320 6.061 1.00 7.28 C
ATOM 92 O3' DA A 5 34.988 36.456 6.830 1.00 7.95 O
ATOM 93 C2' DA A 5 35.028 35.501 4.599 1.00 7.02 C
ATOM 94 C1' DA A 5 35.185 34.047 4.179 1.00 6.99 C
ATOM 95 N9 DA A 5 33.962 33.373 3.730 1.00 6.98 N
ATOM 96 C8 DA A 5 33.331 32.310 4.324 1.00 6.83 C
ATOM 97 N7 DA A 5 32.272 31.890 3.684 1.00 6.48 N
ATOM 98 C5 DA A 5 32.207 32.728 2.581 1.00 6.74 C
ATOM 99 C6 DA A 5 31.308 32.799 1.496 1.00 6.78 C
ATOM 100 N6 DA A 5 30.269 31.973 1.356 1.00 7.73 N
ATOM 101 N1 DA A 5 31.527 33.754 0.563 1.00 6.47 N
ATOM 102 C2 DA A 5 32.568 34.588 0.708 1.00 6.79 C
ATOM 103 N3 DA A 5 33.482 34.609 1.683 1.00 7.00 N
ATOM 104 C4 DA A 5 33.243 33.648 2.590 1.00 6.90 C
ATOM 105 P DC A 6 33.841 37.463 7.312 1.00 8.67 P
ATOM 106 OP1 DC A 6 34.510 38.533 8.086 1.00 10.25 O
ATOM 107 OP2 DC A 6 32.725 36.701 7.902 1.00 9.64 O
ATOM 108 O5' DC A 6 33.299 38.098 5.953 1.00 8.66 O
ATOM 109 C5' DC A 6 34.115 38.996 5.212 1.00 8.90 C
ATOM 110 C4' DC A 6 33.433 39.330 3.903 1.00 8.84 C
ATOM 111 O4' DC A 6 33.276 38.127 3.112 1.00 8.37 O
ATOM 112 C3' DC A 6 32.008 39.846 4.052 1.00 9.06 C
ATOM 113 O3' DC A 6 31.997 41.215 4.436 1.00 11.60 O
ATOM 114 C2' DC A 6 31.474 39.623 2.646 1.00 9.16 C
ATOM 115 C1' DC A 6 32.063 38.243 2.378 1.00 8.32 C
ATOM 116 N1 DC A 6 31.150 37.101 2.714 1.00 7.75 N
ATOM 117 C2 DC A 6 30.116 36.786 1.819 1.00 7.70 C
ATOM 118 O2 DC A 6 29.989 37.475 0.796 1.00 7.91 O
ATOM 119 N3 DC A 6 29.291 35.742 2.101 1.00 7.18 N
ATOM 120 C4 DC A 6 29.457 35.031 3.220 1.00 7.76 C
ATOM 121 N4 DC A 6 28.618 34.015 3.441 1.00 8.11 N
ATOM 122 C5 DC A 6 30.498 35.334 4.154 1.00 7.58 C
ATOM 123 C6 DC A 6 31.310 36.364 3.862 1.00 7.28 C
ATOM 124 P DA A 7 30.748 41.815 5.233 1.00 12.50 P
ATOM 125 OP1 DA A 7 31.143 43.167 5.712 1.00 13.31 O
ATOM 126 OP2 DA A 7 30.200 40.812 6.184 1.00 12.61 O
ATOM 127 O5' DA A 7 29.674 41.979 4.066 1.00 10.71 O
ATOM 128 C5' DA A 7 29.871 42.930 3.021 1.00 10.74 C
ATOM 129 C4' DA A 7 28.691 42.841 2.080 1.00 10.31 C
ATOM 130 O4' DA A 7 28.595 41.503 1.539 1.00 10.39 O
ATOM 131 C3' DA A 7 27.355 43.064 2.759 1.00 10.10 C
ATOM 132 O3' DA A 7 27.099 44.453 2.799 1.00 11.17 O
ATOM 133 C2' DA A 7 26.372 42.323 1.866 1.00 9.62 C
ATOM 134 C1' DA A 7 27.228 41.153 1.415 1.00 8.62 C
ATOM 135 N9 DA A 7 27.059 39.889 2.126 1.00 7.80 N
ATOM 136 C8 DA A 7 27.800 39.405 3.176 1.00 7.82 C
ATOM 137 N7 DA A 7 27.417 38.216 3.582 1.00 7.61 N
ATOM 138 C5 DA A 7 26.367 37.889 2.732 1.00 7.83 C
ATOM 139 C6 DA A 7 25.528 36.753 2.631 1.00 7.91 C
ATOM 140 N6 DA A 7 25.646 35.687 3.429 1.00 7.48 N
ATOM 141 N1 DA A 7 24.565 36.759 1.671 1.00 7.87 N
ATOM 142 C2 DA A 7 24.451 37.829 0.872 1.00 8.14 C
ATOM 143 N3 DA A 7 25.180 38.948 0.868 1.00 8.36 N
ATOM 144 C4 DA A 7 26.129 38.914 1.832 1.00 7.77 C
ATOM 145 P DC A 8 26.210 45.061 3.972 1.00 12.05 P
ATOM 146 OP1 DC A 8 26.241 46.534 3.785 1.00 13.06 O
ATOM 147 OP2 DC A 8 26.633 44.487 5.270 1.00 13.42 O
ATOM 148 O5' DC A 8 24.739 44.550 3.635 1.00 10.98 O
ATOM 149 C5' DC A 8 24.082 45.070 2.478 1.00 12.10 C
ATOM 150 C4' DC A 8 22.739 44.413 2.247 1.00 12.17 C
ATOM 151 O4' DC A 8 22.941 42.978 2.152 1.00 11.58 O
ATOM 152 C3' DC A 8 21.697 44.661 3.337 1.00 13.10 C
ATOM 153 O3' DC A 8 20.459 45.014 2.731 1.00 15.88 O
ATOM 154 C2' DC A 8 21.588 43.326 4.064 1.00 12.36 C
ATOM 155 C1' DC A 8 22.026 42.318 3.000 1.00 11.18 C
ATOM 156 N1 DC A 8 22.660 41.111 3.609 1.00 10.63 N
ATOM 157 C2 DC A 8 22.120 39.835 3.369 1.00 10.15 C
ATOM 158 O2 DC A 8 21.129 39.713 2.636 1.00 10.11 O
ATOM 159 N3 DC A 8 22.703 38.758 3.962 1.00 9.75 N
ATOM 160 C4 DC A 8 23.775 38.913 4.752 1.00 9.68 C
ATOM 161 N4 DC A 8 24.308 37.819 5.314 1.00 9.22 N
ATOM 162 C5 DC A 8 24.348 40.201 4.997 1.00 9.76 C
ATOM 163 C6 DC A 8 23.760 41.254 4.418 1.00 10.05 C
TER 164 DC A 8
HETATM 165 MG MG A 11 30.594 21.925 2.266 1.00 31.29 MG
HETATM 166 O HOH A 21 26.127 47.810 1.437 1.00 13.71 O
HETATM 167 O HOH A 22 26.150 16.493 -0.750 1.00 14.32 O
HETATM 168 O HOH A 23 20.901 38.797 -0.009 1.00 14.62 O
HETATM 169 O HOH A 24 31.380 25.824 -2.831 1.00 12.64 O
HETATM 170 O HOH A 25 30.001 31.134 4.980 1.00 22.12 O
HETATM 171 O HOH A 26 30.445 24.463 6.091 1.00 21.24 O
HETATM 172 O HOH A 27 28.446 19.637 -7.900 1.00 16.25 O
HETATM 173 O HOH A 28 27.354 16.965 -8.501 1.00 13.17 O
HETATM 174 O HOH A 29 17.937 38.605 0.026 1.00 20.65 O
HETATM 175 O HOH A 30 22.697 39.803 -2.060 1.00 19.48 O
HETATM 176 O HOH A 31 38.849 16.919 -2.726 1.00 16.74 O
HETATM 177 O HOH A 32 30.500 24.434 -0.487 1.00 20.02 O
HETATM 178 O HOH A 33 24.599 15.506 1.395 1.00 23.24 O
HETATM 179 O HOH A 34 31.516 34.034 7.443 1.00 17.86 O
HETATM 180 O HOH A 35 25.912 42.750 7.039 1.00 21.98 O
HETATM 181 O HOH A 36 29.131 21.894 0.102 1.00 21.99 O
HETATM 182 O HOH A 37 31.412 22.863 -6.608 1.00 25.02 O
HETATM 183 O HOH A 38 28.058 16.946 2.594 1.00 23.32 O
HETATM 184 O HOH A 39 36.191 22.681 8.803 1.00 29.16 O
HETATM 185 O HOH A 40 31.869 31.924 8.993 1.00 24.12 O
HETATM 186 O HOH A 41 33.958 24.660 -6.285 1.00 20.77 O
HETATM 187 O HOH A 42 27.858 20.417 -3.417 1.00 25.85 O
HETATM 188 O HOH A 43 27.643 40.706 7.127 1.00 23.54 O
HETATM 189 O HOH A 44 33.491 35.652 10.465 1.00 21.88 O
HETATM 190 O HOH A 45 29.641 24.046 3.599 1.00 23.74 O
HETATM 191 O HOH A 46 28.934 33.312 6.511 1.00 32.35 O
HETATM 192 O HOH A 47 27.987 36.709 5.986 1.00 22.00 O
HETATM 193 O HOH A 48 31.394 15.811 5.287 1.00 20.11 O
HETATM 194 O HOH A 49 28.330 29.985 2.990 1.00 26.87 O
HETATM 195 O HOH A 50 30.282 37.852 7.579 1.00 28.99 O
HETATM 196 O HOH A 51 29.414 28.245 1.159 1.00 25.65 O
HETATM 197 O HOH A 52 28.847 15.069 4.238 1.00 25.43 O
HETATM 198 O HOH A 53 28.955 45.075 6.394 1.00 30.65 O
HETATM 199 O HOH A 54 32.407 28.590 7.481 1.00 30.58 O
HETATM 200 O HOH A 55 37.313 21.663 6.220 1.00 33.94 O
HETATM 201 O HOH A 56 31.532 25.157 10.542 1.00 40.65 O
HETATM 202 O HOH A 57 35.859 36.172 1.345 1.00 8.40 O
HETATM 203 O HOH A 58 23.926 41.410 -0.257 1.00 14.40 O
CONECT 6 20
CONECT 20 6 21 22 23
CONECT 21 20
CONECT 22 20
CONECT 23 20 24
CONECT 24 23 25
CONECT 25 24 26 27
CONECT 26 25 31
CONECT 27 25 28 29
CONECT 28 27 41
CONECT 29 27 30 31
CONECT 30 29 32
CONECT 31 26 29 33
CONECT 32 30
CONECT 33 31 34 40
CONECT 34 33 35 36
CONECT 35 34
CONECT 36 34 37
CONECT 37 36 38 39
CONECT 38 37
CONECT 39 37 40
CONECT 40 33 39
CONECT 41 28
CONECT 43 165
CONECT 49 63
CONECT 63 49 81 82 83
CONECT 64 65 66 74
CONECT 65 64 71
CONECT 66 64 67 68
CONECT 67 66
CONECT 68 66 69
CONECT 69 68 70 71
CONECT 70 69
CONECT 71 65 69 72
CONECT 72 71 73
CONECT 73 72
CONECT 74 64 75 79
CONECT 75 74 76
CONECT 76 75 77 80
CONECT 77 76 78 79
CONECT 78 77 84
CONECT 79 74 77
CONECT 80 76 81
CONECT 81 63 80
CONECT 82 63
CONECT 83 63
CONECT 84 78
CONECT 165 43 181 190
CONECT 181 165
CONECT 190 165
MASTER 316 0 3 0 0 0 1 6 202 1 50 1
END