HEADER DNA 16-FEB-10 3LTR
TITLE 5-OME-DU CONTAINING DNA 8MER
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*(UMS)P*GP*(T5O)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 SYNTHESIZER
KEYWDS DNA, OLIGONUCLEOTIDE, 2'-SEME, 5-OME, SELENIUM, 5-METHOXY-URIDINE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.SHENG,A.E.A.HASSAN,W.ZHANG,J.GAN,Z.HUANG
REVDAT 5 06-SEP-23 3LTR 1 REMARK LINK
REVDAT 4 26-SEP-12 3LTR 1 JRNL
REVDAT 3 13-JUN-12 3LTR 1 JRNL
REVDAT 2 13-JUL-11 3LTR 1 VERSN
REVDAT 1 09-MAR-10 3LTR 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. 1.30 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) : 1.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.40
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1
REMARK 3 NUMBER OF REFLECTIONS : 5117
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) : 0.203
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.222
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600
REMARK 3 FREE R VALUE TEST SET COUNT : 246
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) : 1.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33
REMARK 3 REFLECTION IN BIN (WORKING SET) : 174
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 43.90
REMARK 3 BIN R VALUE (WORKING SET) : 0.3960
REMARK 3 BIN FREE R VALUE SET COUNT : 13
REMARK 3 BIN FREE R VALUE : 0.4230
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 : 42
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) : 13.10
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.25000
REMARK 3 B22 (A**2) : -0.25000
REMARK 3 B33 (A**2) : 0.50000
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): 0.060
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.061
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.984
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 182 ; 0.006 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 278 ; 1.251 ; 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): 32 ; 0.060 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 83 ; 0.008 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 59 ; 0.158 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 108 ; 0.276 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 28 ; 0.151 ; 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): 19 ; 0.187 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.088 ; 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 ; 0.895 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 278 ; 1.318 ; 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): 11.4486 12.5770 2.4137
REMARK 3 T TENSOR
REMARK 3 T11: 0.0704 T22: 0.0549
REMARK 3 T33: 0.0671 T12: -0.0063
REMARK 3 T13: -0.0152 T23: 0.0005
REMARK 3 L TENSOR
REMARK 3 L11: 0.9159 L22: 3.9115
REMARK 3 L33: 0.4272 L12: -1.0744
REMARK 3 L13: 0.1786 L23: -0.8824
REMARK 3 S TENSOR
REMARK 3 S11: -0.0595 S12: -0.0351 S13: -0.0042
REMARK 3 S21: 0.2754 S22: 0.0474 S23: -0.0337
REMARK 3 S31: -0.0654 S32: 0.0470 S33: 0.0120
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 3LTR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-10.
REMARK 100 THE DEPOSITION ID IS D_1000057719.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-JUL-09
REMARK 200 TEMPERATURE (KELVIN) : 99
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X12C
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 : SI(111)
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5389
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300
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 (%) : 91.0
REMARK 200 DATA REDUNDANCY : 21.50
REMARK 200 R MERGE (I) : 0.06000
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 36.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35
REMARK 200 COMPLETENESS FOR SHELL (%) : 58.1
REMARK 200 DATA REDUNDANCY IN SHELL : 5.50
REMARK 200 R MERGE FOR SHELL (I) : 0.38100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 2.000
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 (%): 43.65
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V / V MPD, 40 MM NA CACODYLATE PH
REMARK 280 6.0,12 MM SPERMINE TETRA-HCL, 80 MM SODIUM CHLORIDE, 20 MM
REMARK 280 MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 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 11.91100
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.49600
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.49600
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.86650
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.49600
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.49600
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 5.95550
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.49600
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.49600
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.86650
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.49600
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.49600
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 5.95550
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 11.91100
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: 2250 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 2810 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.3 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 UMS A 2 O4
REMARK 620 2 DG A 3 O6 70.7
REMARK 620 3 HOH A 120 O 80.2 89.7
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
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3IJK RELATED DB: PDB
REMARK 900 RELATED ID: 3LTU RELATED DB: PDB
DBREF 3LTR A 1 8 PDB 3LTR 3LTR 1 8
SEQRES 1 A 8 DG UMS DG T5O DA DC DA DC
MODRES 3LTR UMS A 2 DU
MODRES 3LTR T5O A 4 DU
HET UMS A 2 21
HET T5O A 4 21
HET MG A 11 1
HETNAM UMS 2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE
HETNAM T5O 2'-DEOXY-5-METHOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)
HETNAM MG MAGNESIUM ION
HETSYN T5O 5-METHOXY-2'-DEOXYURIDINE-5'-PHOSPHATE
FORMUL 1 UMS C10 H15 N2 O8 P SE
FORMUL 1 T5O C10 H15 N2 O9 P
FORMUL 2 MG MG 2+
FORMUL 3 HOH *42(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 O4 UMS A 2 MG MG A 11 1555 1555 2.90
LINK O6 DG A 3 MG MG A 11 1555 1555 2.93
LINK MG MG A 11 O HOH A 120 1555 1555 2.63
SITE 1 AC1 3 UMS A 2 DG A 3 HOH A 120
CRYST1 42.992 42.992 23.822 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 0.023260 0.000000 0.000000 0.00000
SCALE2 0.000000 0.023260 0.000000 0.00000
SCALE3 0.000000 0.000000 0.041978 0.00000
ATOM 1 O5' DG A 1 13.558 24.251 -5.233 1.00 9.93 O
ATOM 2 C5' DG A 1 13.620 25.638 -4.952 1.00 8.29 C
ATOM 3 C4' DG A 1 12.348 26.114 -4.270 1.00 8.09 C
ATOM 4 O4' DG A 1 11.184 25.891 -5.112 1.00 7.48 O
ATOM 5 C3' DG A 1 12.003 25.426 -2.952 1.00 8.05 C
ATOM 6 O3' DG A 1 12.761 25.987 -1.871 1.00 8.29 O
ATOM 7 C2' DG A 1 10.515 25.741 -2.857 1.00 8.91 C
ATOM 8 C1' DG A 1 10.078 25.543 -4.307 1.00 8.63 C
ATOM 9 N9 DG A 1 9.718 24.156 -4.590 1.00 8.08 N
ATOM 10 C8 DG A 1 10.491 23.199 -5.206 1.00 8.34 C
ATOM 11 N7 DG A 1 9.898 22.046 -5.313 1.00 8.34 N
ATOM 12 C5 DG A 1 8.661 22.244 -4.718 1.00 8.51 C
ATOM 13 C6 DG A 1 7.580 21.351 -4.538 1.00 9.12 C
ATOM 14 O6 DG A 1 7.514 20.165 -4.882 1.00 9.20 O
ATOM 15 N1 DG A 1 6.497 21.945 -3.889 1.00 8.43 N
ATOM 16 C2 DG A 1 6.468 23.260 -3.479 1.00 8.47 C
ATOM 17 N2 DG A 1 5.347 23.683 -2.874 1.00 9.34 N
ATOM 18 N3 DG A 1 7.476 24.112 -3.644 1.00 9.06 N
ATOM 19 C4 DG A 1 8.534 23.540 -4.269 1.00 8.41 C
HETATM 20 P UMS A 2 13.245 25.068 -0.653 1.00 9.37 P
HETATM 21 OP1 UMS A 2 14.103 25.936 0.176 1.00 9.05 O
HETATM 22 OP2 UMS A 2 13.760 23.782 -1.162 1.00 9.70 O
HETATM 23 O5' UMS A 2 11.895 24.737 0.142 1.00 8.81 O
HETATM 24 C5' UMS A 2 11.208 25.765 0.822 1.00 9.14 C
HETATM 25 C4' UMS A 2 9.878 25.254 1.321 1.00 9.91 C
HETATM 26 O4' UMS A 2 9.076 24.820 0.189 1.00 8.68 O
HETATM 27 C3' UMS A 2 9.961 24.055 2.255 1.00 10.92 C
HETATM 28 O3' UMS A 2 10.227 24.540 3.573 1.00 13.28 O
HETATM 29 C2' UMS A 2 8.557 23.477 2.086 1.00 10.03 C
HETATM 30 SE2' UMS A 2 7.229 24.438 3.189 0.90 13.07 SE
HETATM 31 C1' UMS A 2 8.288 23.719 0.593 1.00 8.91 C
HETATM 32 CA' UMS A 2 5.608 23.352 3.001 0.90 11.50 C
HETATM 33 N1 UMS A 2 8.623 22.522 -0.255 1.00 8.59 N
HETATM 34 C2 UMS A 2 7.691 21.505 -0.354 1.00 8.06 C
HETATM 35 O2 UMS A 2 6.604 21.539 0.201 1.00 8.93 O
HETATM 36 N3 UMS A 2 8.075 20.443 -1.141 1.00 8.00 N
HETATM 37 C4 UMS A 2 9.280 20.283 -1.819 1.00 8.43 C
HETATM 38 O4 UMS A 2 9.477 19.266 -2.483 1.00 9.02 O
HETATM 39 C5 UMS A 2 10.209 21.380 -1.661 1.00 8.29 C
HETATM 40 C6 UMS A 2 9.852 22.430 -0.898 1.00 8.32 C
ATOM 41 P DG A 3 10.956 23.656 4.688 1.00 15.86 P
ATOM 42 OP1 DG A 3 11.224 24.534 5.842 1.00 17.02 O
ATOM 43 OP2 DG A 3 12.032 22.879 4.063 1.00 15.67 O
ATOM 44 O5' DG A 3 9.768 22.657 5.074 1.00 15.02 O
ATOM 45 C5' DG A 3 9.924 21.274 5.044 1.00 13.99 C
ATOM 46 C4' DG A 3 8.546 20.656 5.109 1.00 13.16 C
ATOM 47 O4' DG A 3 7.907 20.784 3.812 1.00 12.03 O
ATOM 48 C3' DG A 3 8.587 19.171 5.406 1.00 12.80 C
ATOM 49 O3' DG A 3 8.554 18.965 6.821 1.00 13.31 O
ATOM 50 C2' DG A 3 7.341 18.683 4.673 1.00 11.86 C
ATOM 51 C1' DG A 3 7.382 19.534 3.404 1.00 10.60 C
ATOM 52 N9 DG A 3 8.200 18.956 2.331 1.00 10.15 N
ATOM 53 C8 DG A 3 9.415 19.377 1.841 1.00 9.99 C
ATOM 54 N7 DG A 3 9.881 18.630 0.878 1.00 9.73 N
ATOM 55 C5 DG A 3 8.911 17.649 0.715 1.00 9.15 C
ATOM 56 C6 DG A 3 8.845 16.555 -0.183 1.00 9.38 C
ATOM 57 O6 DG A 3 9.670 16.228 -1.038 1.00 9.37 O
ATOM 58 N1 DG A 3 7.686 15.796 -0.022 1.00 8.96 N
ATOM 59 C2 DG A 3 6.704 16.067 0.895 1.00 9.30 C
ATOM 60 N2 DG A 3 5.654 15.240 0.910 1.00 9.41 N
ATOM 61 N3 DG A 3 6.749 17.090 1.741 1.00 9.25 N
ATOM 62 C4 DG A 3 7.874 17.839 1.595 1.00 9.24 C
HETATM 63 P T5O A 4 9.241 17.686 7.495 1.00 13.62 P
HETATM 64 N1 T5O A 4 7.898 14.079 3.531 1.00 9.55 N
HETATM 65 C2 T5O A 4 7.982 13.157 2.505 1.00 8.96 C
HETATM 66 O2 T5O A 4 7.123 12.327 2.278 1.00 9.62 O
HETATM 67 N3 T5O A 4 9.115 13.244 1.741 1.00 8.52 N
HETATM 68 C4 T5O A 4 10.161 14.130 1.915 1.00 9.42 C
HETATM 69 O4 T5O A 4 11.150 14.131 1.185 1.00 9.76 O
HETATM 70 C5 T5O A 4 10.027 15.065 3.006 1.00 10.14 C
HETATM 71 O5 T5O A 4 11.105 15.985 3.179 1.00 12.09 O
HETATM 72 C6 T5O A 4 8.915 15.000 3.761 1.00 9.90 C
HETATM 73 C1' T5O A 4 6.666 14.050 4.400 1.00 9.86 C
HETATM 74 C2' T5O A 4 6.709 12.982 5.490 1.00 9.62 C
HETATM 75 OP2 T5O A 4 10.636 17.554 7.062 1.00 13.85 O
HETATM 76 C3' T5O A 4 7.182 13.802 6.686 1.00 9.38 C
HETATM 77 O3' T5O A 4 6.786 13.243 7.931 1.00 9.35 O
HETATM 78 C4' T5O A 4 6.433 15.110 6.465 1.00 10.09 C
HETATM 79 O4' T5O A 4 6.486 15.310 5.030 1.00 10.71 O
HETATM 80 C5' T5O A 4 7.008 16.317 7.187 1.00 11.25 C
HETATM 81 O5' T5O A 4 8.393 16.480 6.874 1.00 12.36 O
HETATM 82 C7 T5O A 4 10.840 17.002 4.138 1.00 13.86 C
HETATM 83 OP1 T5O A 4 8.969 17.750 8.948 1.00 15.35 O
ATOM 84 P DA A 5 7.688 12.150 8.665 1.00 11.16 P
ATOM 85 OP1 DA A 5 7.191 12.132 10.053 1.00 12.29 O
ATOM 86 OP2 DA A 5 9.114 12.406 8.399 1.00 12.20 O
ATOM 87 O5' DA A 5 7.254 10.792 7.932 1.00 8.59 O
ATOM 88 C5' DA A 5 8.163 9.752 7.634 1.00 7.29 C
ATOM 89 C4' DA A 5 7.601 8.925 6.498 1.00 7.09 C
ATOM 90 O4' DA A 5 7.477 9.748 5.314 1.00 7.95 O
ATOM 91 C3' DA A 5 8.492 7.765 6.092 1.00 6.84 C
ATOM 92 O3' DA A 5 8.154 6.623 6.854 1.00 7.21 O
ATOM 93 C2' DA A 5 8.160 7.591 4.615 1.00 6.87 C
ATOM 94 C1' DA A 5 7.994 9.043 4.199 1.00 6.97 C
ATOM 95 N9 DA A 5 9.207 9.719 3.735 1.00 6.74 N
ATOM 96 C8 DA A 5 9.836 10.781 4.321 1.00 7.53 C
ATOM 97 N7 DA A 5 10.887 11.202 3.659 1.00 7.50 N
ATOM 98 C5 DA A 5 10.949 10.368 2.559 1.00 7.10 C
ATOM 99 C6 DA A 5 11.836 10.300 1.461 1.00 6.89 C
ATOM 100 N6 DA A 5 12.867 11.135 1.298 1.00 7.26 N
ATOM 101 N1 DA A 5 11.606 9.347 0.528 1.00 6.18 N
ATOM 102 C2 DA A 5 10.572 8.513 0.687 1.00 7.11 C
ATOM 103 N3 DA A 5 9.678 8.486 1.680 1.00 6.58 N
ATOM 104 C4 DA A 5 9.920 9.441 2.586 1.00 6.34 C
ATOM 105 P DC A 6 9.281 5.604 7.326 1.00 8.10 P
ATOM 106 OP1 DC A 6 8.604 4.538 8.086 1.00 9.42 O
ATOM 107 OP2 DC A 6 10.389 6.375 7.924 1.00 8.62 O
ATOM 108 O5' DC A 6 9.811 4.995 5.956 1.00 7.74 O
ATOM 109 C5' DC A 6 8.999 4.081 5.237 1.00 7.92 C
ATOM 110 C4' DC A 6 9.645 3.740 3.911 1.00 8.59 C
ATOM 111 O4' DC A 6 9.816 4.930 3.105 1.00 8.23 O
ATOM 112 C3' DC A 6 11.055 3.193 4.035 1.00 8.87 C
ATOM 113 O3' DC A 6 11.009 1.836 4.440 1.00 9.75 O
ATOM 114 C2' DC A 6 11.563 3.395 2.614 1.00 8.24 C
ATOM 115 C1' DC A 6 11.001 4.782 2.329 1.00 7.93 C
ATOM 116 N1 DC A 6 11.937 5.910 2.650 1.00 6.18 N
ATOM 117 C2 DC A 6 12.970 6.197 1.744 1.00 6.71 C
ATOM 118 O2 DC A 6 13.086 5.488 0.732 1.00 7.58 O
ATOM 119 N3 DC A 6 13.805 7.230 2.014 1.00 6.41 N
ATOM 120 C4 DC A 6 13.661 7.959 3.125 1.00 6.59 C
ATOM 121 N4 DC A 6 14.518 8.961 3.329 1.00 7.44 N
ATOM 122 C5 DC A 6 12.617 7.692 4.064 1.00 6.26 C
ATOM 123 C6 DC A 6 11.792 6.671 3.787 1.00 5.93 C
ATOM 124 P DA A 7 12.230 1.179 5.234 1.00 10.31 P
ATOM 125 OP1 DA A 7 11.753 -0.151 5.697 1.00 11.31 O
ATOM 126 OP2 DA A 7 12.821 2.160 6.175 1.00 9.74 O
ATOM 127 O5' DA A 7 13.300 0.969 4.066 1.00 9.28 O
ATOM 128 C5' DA A 7 13.065 0.053 2.991 1.00 10.37 C
ATOM 129 C4' DA A 7 14.242 0.091 2.033 1.00 8.76 C
ATOM 130 O4' DA A 7 14.366 1.415 1.464 1.00 9.14 O
ATOM 131 C3' DA A 7 15.592 -0.164 2.690 1.00 9.04 C
ATOM 132 O3' DA A 7 15.817 -1.554 2.743 1.00 9.04 O
ATOM 133 C2' DA A 7 16.574 0.545 1.769 1.00 8.66 C
ATOM 134 C1' DA A 7 15.738 1.731 1.324 1.00 7.42 C
ATOM 135 N9 DA A 7 15.941 2.995 2.022 1.00 6.62 N
ATOM 136 C8 DA A 7 15.207 3.495 3.068 1.00 6.07 C
ATOM 137 N7 DA A 7 15.602 4.688 3.446 1.00 6.16 N
ATOM 138 C5 DA A 7 16.658 4.993 2.589 1.00 5.63 C
ATOM 139 C6 DA A 7 17.500 6.119 2.461 1.00 6.73 C
ATOM 140 N6 DA A 7 17.403 7.205 3.241 1.00 5.69 N
ATOM 141 N1 DA A 7 18.447 6.084 1.493 1.00 6.44 N
ATOM 142 C2 DA A 7 18.547 5.005 0.705 1.00 6.88 C
ATOM 143 N3 DA A 7 17.805 3.895 0.722 1.00 6.91 N
ATOM 144 C4 DA A 7 16.873 3.955 1.695 1.00 6.29 C
ATOM 145 P DC A 8 16.747 -2.165 3.895 1.00 11.00 P
ATOM 146 OP1 DC A 8 16.691 -3.641 3.775 1.00 11.06 O
ATOM 147 OP2 DC A 8 16.377 -1.560 5.192 1.00 12.34 O
ATOM 148 O5' DC A 8 18.211 -1.669 3.500 1.00 9.57 O
ATOM 149 C5' DC A 8 18.833 -2.187 2.334 1.00 9.10 C
ATOM 150 C4' DC A 8 20.183 -1.539 2.137 1.00 8.71 C
ATOM 151 O4' DC A 8 19.992 -0.103 2.088 1.00 8.67 O
ATOM 152 C3' DC A 8 21.194 -1.817 3.250 1.00 9.51 C
ATOM 153 O3' DC A 8 22.458 -2.161 2.706 1.00 11.59 O
ATOM 154 C2' DC A 8 21.291 -0.490 4.001 1.00 9.81 C
ATOM 155 C1' DC A 8 20.919 0.537 2.931 1.00 7.99 C
ATOM 156 N1 DC A 8 20.302 1.759 3.530 1.00 7.51 N
ATOM 157 C2 DC A 8 20.859 3.030 3.299 1.00 6.91 C
ATOM 158 O2 DC A 8 21.857 3.148 2.576 1.00 7.83 O
ATOM 159 N3 DC A 8 20.279 4.112 3.886 1.00 6.59 N
ATOM 160 C4 DC A 8 19.202 3.973 4.671 1.00 5.93 C
ATOM 161 N4 DC A 8 18.686 5.067 5.235 1.00 6.57 N
ATOM 162 C5 DC A 8 18.610 2.692 4.909 1.00 6.59 C
ATOM 163 C6 DC A 8 19.188 1.630 4.326 1.00 7.02 C
TER 164 DC A 8
HETATM 165 MG MG A 11 11.820 17.566 -2.505 1.00 17.37 MG
HETATM 166 O HOH A 101 7.311 6.981 1.345 1.00 13.74 O
HETATM 167 O HOH A 102 19.030 1.453 -0.301 1.00 16.81 O
HETATM 168 O HOH A 103 16.755 -4.792 1.343 1.00 17.01 O
HETATM 169 O HOH A 104 3.980 22.085 0.100 1.00 18.79 O
HETATM 170 O HOH A 105 13.606 15.491 1.739 1.00 21.38 O
HETATM 171 O HOH A 106 6.198 4.699 2.605 1.00 15.86 O
HETATM 172 O HOH A 107 4.610 17.369 3.449 1.00 21.42 O
HETATM 173 O HOH A 108 14.603 26.219 2.774 1.00 30.39 O
HETATM 174 O HOH A 109 16.595 26.663 -0.909 1.00 19.36 O
HETATM 175 O HOH A 110 3.074 20.319 2.132 1.00 20.39 O
HETATM 176 O HOH A 111 13.138 1.654 9.676 1.00 50.43 O
HETATM 177 O HOH A 112 7.215 2.129 1.849 1.00 20.77 O
HETATM 178 O HOH A 113 3.698 17.046 6.168 1.00 23.72 O
HETATM 179 O HOH A 114 21.298 -4.458 0.984 1.00 23.89 O
HETATM 180 O HOH A 115 4.114 18.897 8.056 1.00 33.61 O
HETATM 181 O HOH A 116 13.524 21.464 0.290 1.00 25.48 O
HETATM 182 O HOH A 117 11.529 20.153 -6.303 1.00 31.98 O
HETATM 183 O HOH A 118 24.115 0.079 1.248 1.00 27.99 O
HETATM 184 O HOH A 119 15.317 2.312 7.035 1.00 26.80 O
HETATM 185 O HOH A 120 12.345 19.023 -0.378 1.00 23.13 O
HETATM 186 O HOH A 121 14.332 10.505 5.851 1.00 28.81 O
HETATM 187 O HOH A 122 15.012 22.988 -3.391 1.00 27.37 O
HETATM 188 O HOH A 123 6.029 3.375 7.226 1.00 25.97 O
HETATM 189 O HOH A 124 17.373 24.783 -4.724 1.00 39.00 O
HETATM 190 O HOH A 125 9.125 18.486 -6.042 1.00 26.65 O
HETATM 191 O HOH A 126 10.949 12.771 6.715 1.00 39.08 O
HETATM 192 O HOH A 127 14.695 13.166 2.623 1.00 38.94 O
HETATM 193 O HOH A 128 11.793 9.000 7.344 1.00 33.24 O
HETATM 194 O HOH A 129 13.018 6.547 7.509 1.00 36.14 O
HETATM 195 O HOH A 130 16.198 7.941 6.055 1.00 25.94 O
HETATM 196 O HOH A 131 14.890 5.901 5.775 1.00 25.35 O
HETATM 197 O HOH A 132 12.670 19.162 6.246 1.00 30.67 O
HETATM 198 O HOH A 133 12.908 12.739 4.593 1.00 28.26 O
HETATM 199 O HOH A 134 11.531 27.221 5.330 1.00 27.77 O
HETATM 200 O HOH A 135 13.817 -2.065 6.433 1.00 41.50 O
HETATM 201 O HOH A 136 9.741 7.473 10.481 1.00 30.74 O
HETATM 202 O HOH A 137 13.269 19.518 3.927 1.00 31.29 O
HETATM 203 O HOH A 138 12.118 21.298 2.367 1.00 28.09 O
HETATM 204 O HOH A 139 13.249 4.243 10.630 1.00 34.84 O
HETATM 205 O HOH A 140 12.038 15.096 7.313 1.00 32.26 O
HETATM 206 O HOH A 141 11.220 10.898 9.048 1.00 40.58 O
HETATM 207 O HOH A 142 15.860 -3.262 7.737 1.00 38.94 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 37 165
CONECT 39 37 40
CONECT 40 33 39
CONECT 41 28
CONECT 57 165
CONECT 63 75 81 83
CONECT 64 65 72 73
CONECT 65 64 66 67
CONECT 66 65
CONECT 67 65 68
CONECT 68 67 69 70
CONECT 69 68
CONECT 70 68 71 72
CONECT 71 70 82
CONECT 72 64 70
CONECT 73 64 74 79
CONECT 74 73 76
CONECT 75 63
CONECT 76 74 77 78
CONECT 77 76
CONECT 78 76 79 80
CONECT 79 73 78
CONECT 80 78 81
CONECT 81 63 80
CONECT 82 71
CONECT 83 63
CONECT 165 38 57 185
CONECT 185 165
MASTER 319 0 3 0 0 0 1 6 206 1 47 1
END