HEADER DNA 17-NOV-09 3KQ8
TITLE 5-TE-URIDINE DERIVATIZED DNA-8MER
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*(UMS)P*GP*(TTI)P*AP*CP*AP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: 5-TELLURIUM MODIFIED DNA
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZE 5-TE-URIDINE AND INCORPORATED
SOURCE 4 IT INTO DNA
KEYWDS TELLURIUM DNA, DNA
EXPDTA X-RAY DIFFRACTION
AUTHOR J.SHENG,A.E.A.HASSAN,W.ZHANG,Z.HUANG
REVDAT 2 21-FEB-24 3KQ8 1 REMARK LINK
REVDAT 1 17-NOV-10 3KQ8 0
JRNL AUTH J.SHENG,A.E.A.HASSAN,W.ZHANG,Z.HUANG
JRNL TITL SYNTHESIS AND STRUCTURE STUDIES OF 5-TELLURIUM MODIFIED DNA
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.60 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) : 1.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.87
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0
REMARK 3 NUMBER OF REFLECTIONS : 2965
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) : 0.189
REMARK 3 R VALUE (WORKING SET) : 0.186
REMARK 3 FREE R VALUE : 0.229
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.300
REMARK 3 FREE R VALUE TEST SET COUNT : 134
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) : 1.60
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64
REMARK 3 REFLECTION IN BIN (WORKING SET) : 192
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.52
REMARK 3 BIN R VALUE (WORKING SET) : 0.2150
REMARK 3 BIN FREE R VALUE SET COUNT : 6
REMARK 3 BIN FREE R VALUE : 0.1700
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 0
REMARK 3 NUCLEIC ACID ATOMS : 162
REMARK 3 HETEROGEN ATOMS : 1
REMARK 3 SOLVENT ATOMS : 36
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.59
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.04000
REMARK 3 B22 (A**2) : -0.04000
REMARK 3 B33 (A**2) : 0.08000
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): 0.092
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.900
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 181 ; 0.007 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 277 ; 1.531 ; 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 ; 0.052 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 83 ; 0.009 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 62 ; 0.139 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 107 ; 0.273 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 22 ; 0.177 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.993 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 22 ; 0.184 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.100 ; 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): 262 ; 1.154 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 277 ; 1.438 ; 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 : 2
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 9
REMARK 3 ORIGIN FOR THE GROUP (A): 40.6005 30.1718 -0.9870
REMARK 3 T TENSOR
REMARK 3 T11: -0.0025 T22: 0.0025
REMARK 3 T33: -0.0204 T12: 0.0032
REMARK 3 T13: -0.0101 T23: -0.0051
REMARK 3 L TENSOR
REMARK 3 L11: 10.0892 L22: 0.1978
REMARK 3 L33: 0.2103 L12: 1.4125
REMARK 3 L13: 1.4568 L23: 0.2040
REMARK 3 S TENSOR
REMARK 3 S11: 0.0216 S12: 0.2862 S13: -0.0008
REMARK 3 S21: -0.0050 S22: -0.0122 S23: 0.0101
REMARK 3 S31: -0.0585 S32: -0.0434 S33: -0.0093
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 5 A 13
REMARK 3 ORIGIN FOR THE GROUP (A): 25.3941 34.4537 -3.8004
REMARK 3 T TENSOR
REMARK 3 T11: -0.0549 T22: -0.0268
REMARK 3 T33: -0.0473 T12: 0.0029
REMARK 3 T13: -0.0052 T23: 0.0172
REMARK 3 L TENSOR
REMARK 3 L11: 5.4551 L22: 3.1225
REMARK 3 L33: 1.9382 L12: -1.9288
REMARK 3 L13: -0.5311 L23: 1.5510
REMARK 3 S TENSOR
REMARK 3 S11: 0.0885 S12: 0.1148 S13: 0.0163
REMARK 3 S21: 0.1310 S22: -0.0537 S23: 0.0200
REMARK 3 S31: 0.1055 S32: -0.1385 S33: -0.0348
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 3KQ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-09.
REMARK 100 THE DEPOSITION ID IS D_1000056310.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 14-NOV-09
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 : X12C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : SI(III)
REMARK 200 OPTICS : NULL
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 : 3122
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600
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 (%) : 99.2
REMARK 200 DATA REDUNDANCY : 22.50
REMARK 200 R MERGE (I) : 0.07400
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 49.7700
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63
REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4
REMARK 200 DATA REDUNDANCY IN SHELL : 7.80
REMARK 200 R MERGE FOR SHELL (I) : 0.18600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 15.50
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD
REMARK 200 SOFTWARE USED: SHELXS
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.62
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V / V MPD, 40 MM NA CACODYLATE PH
REMARK 280 7.0, 12 MM SPERMINE TETRA-HCL, 80 MM POTASSIUM CHLORIDE AND 20
REMARK 280 MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 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 11.96450
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.12100
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.12100
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.94675
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.12100
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.12100
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 5.98225
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.12100
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.12100
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.94675
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.12100
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.12100
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 5.98225
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 11.96450
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: 3450 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 2500 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 O5' - P - OP2 ANGL. DEV. = -5.5 DEGREES
REMARK 500 DG A 3 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES
REMARK 500 DG A 3 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES
REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.5 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 TTI A 4 TE5
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 35 O
REMARK 620 2 TTI A 4 C5 165.7
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 9 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 25 O
REMARK 620 2 HOH A 37 O 108.5
REMARK 620 N 1
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 9
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3FA1 RELATED DB: PDB
DBREF 3KQ8 A 1 8 PDB 3KQ8 3KQ8 1 8
SEQRES 1 A 8 DG UMS DG TTI DA DC DA DC
MODRES 3KQ8 UMS A 2 DU
MODRES 3KQ8 TTI A 4 DU
HET UMS A 2 21
HET TTI A 4 20
HET MG A 9 1
HETNAM UMS 2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE
HETNAM TTI 2'-DEOXY-5-TELLUROXOURIDINE 5'-(DIHYDROGEN PHOSPHATE)
HETNAM MG MAGNESIUM ION
HETSYN TTI 5-TELLURIUM-DEOXYURIDINE-5'-PHOSPHATE
FORMUL 1 UMS C10 H15 N2 O8 P SE
FORMUL 1 TTI C9 H13 N2 O8 P TE
FORMUL 2 MG MG 2+
FORMUL 3 HOH *36(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 1.61
LINK O3' DG A 3 P TTI A 4 1555 1555 1.60
LINK O3' TTI A 4 P DA A 5 1555 1555 1.59
LINK TE5 TTI A 4 O HOH A 35 1555 1555 2.37
LINK MG MG A 9 O HOH A 25 1555 1555 1.86
LINK MG MG A 9 O HOH A 37 1555 1555 1.89
SITE 1 AC1 4 UMS A 2 DG A 3 HOH A 25 HOH A 37
CRYST1 42.242 42.242 23.929 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 0.023673 0.000000 0.000000 0.00000
SCALE2 0.000000 0.023673 0.000000 0.00000
SCALE3 0.000000 0.000000 0.041790 0.00000
ATOM 1 O5' DG A 1 44.387 34.764 5.379 1.00 11.06 O
ATOM 2 C5' DG A 1 45.797 34.857 5.116 1.00 11.86 C
ATOM 3 C4' DG A 1 46.331 33.658 4.347 1.00 11.68 C
ATOM 4 O4' DG A 1 46.195 32.457 5.156 1.00 11.44 O
ATOM 5 C3' DG A 1 45.609 33.303 3.052 1.00 11.52 C
ATOM 6 O3' DG A 1 46.118 34.119 2.002 1.00 12.27 O
ATOM 7 C2' DG A 1 45.997 31.830 2.902 1.00 11.47 C
ATOM 8 C1' DG A 1 45.839 31.358 4.341 1.00 11.32 C
ATOM 9 N9 DG A 1 44.468 30.948 4.657 1.00 11.68 N
ATOM 10 C8 DG A 1 43.485 31.679 5.282 1.00 11.54 C
ATOM 11 N7 DG A 1 42.355 31.036 5.406 1.00 12.25 N
ATOM 12 C5 DG A 1 42.613 29.799 4.809 1.00 11.01 C
ATOM 13 C6 DG A 1 41.777 28.671 4.631 1.00 11.02 C
ATOM 14 O6 DG A 1 40.604 28.545 4.997 1.00 11.70 O
ATOM 15 N1 DG A 1 42.437 27.610 3.988 1.00 11.02 N
ATOM 16 C2 DG A 1 43.745 27.658 3.558 1.00 12.29 C
ATOM 17 N2 DG A 1 44.233 26.563 2.959 1.00 12.54 N
ATOM 18 N3 DG A 1 44.536 28.708 3.723 1.00 10.54 N
ATOM 19 C4 DG A 1 43.903 29.735 4.335 1.00 10.82 C
HETATM 20 P UMS A 2 45.187 34.585 0.789 1.00 11.64 P
HETATM 21 OP1 UMS A 2 46.009 35.447 -0.069 1.00 11.77 O
HETATM 22 OP2 UMS A 2 43.881 35.040 1.303 1.00 12.03 O
HETATM 23 O5' UMS A 2 44.907 33.255 -0.049 1.00 11.28 O
HETATM 24 C5' UMS A 2 45.922 32.613 -0.800 1.00 10.57 C
HETATM 25 C4' UMS A 2 45.449 31.255 -1.265 1.00 12.64 C
HETATM 26 O4' UMS A 2 45.079 30.429 -0.136 1.00 12.41 O
HETATM 27 C3' UMS A 2 44.195 31.265 -2.127 1.00 14.22 C
HETATM 28 O3' UMS A 2 44.542 31.649 -3.442 1.00 16.87 O
HETATM 29 C2' UMS A 2 43.758 29.806 -2.014 1.00 14.05 C
HETATM 30 SE2' UMS A 2 44.913 28.605 -3.081 1.00 15.73 SE
HETATM 31 C1' UMS A 2 44.036 29.563 -0.532 1.00 13.07 C
HETATM 32 CA' UMS A 2 43.932 26.909 -3.107 1.00 17.55 C
HETATM 33 N1 UMS A 2 42.847 29.839 0.321 1.00 13.63 N
HETATM 34 C2 UMS A 2 41.881 28.843 0.426 1.00 13.61 C
HETATM 35 O2 UMS A 2 41.973 27.772 -0.155 1.00 13.74 O
HETATM 36 N3 UMS A 2 40.814 29.154 1.243 1.00 12.01 N
HETATM 37 C4 UMS A 2 40.625 30.347 1.928 1.00 12.26 C
HETATM 38 O4 UMS A 2 39.618 30.490 2.604 1.00 11.98 O
HETATM 39 C5 UMS A 2 41.666 31.344 1.775 1.00 12.65 C
HETATM 40 C6 UMS A 2 42.718 31.058 0.986 1.00 12.76 C
ATOM 41 P DG A 3 43.517 32.397 -4.431 1.00 17.88 P
ATOM 42 OP1 DG A 3 44.288 32.623 -5.656 1.00 19.84 O
ATOM 43 OP2 DG A 3 42.907 33.520 -3.693 1.00 19.81 O
ATOM 44 O5' DG A 3 42.240 31.431 -4.584 1.00 20.13 O
ATOM 45 C5' DG A 3 42.154 30.353 -5.486 1.00 20.14 C
ATOM 46 C4' DG A 3 41.060 29.378 -5.060 1.00 16.04 C
ATOM 47 O4' DG A 3 41.063 29.180 -3.623 1.00 15.24 O
ATOM 48 C3' DG A 3 39.600 29.734 -5.321 1.00 14.35 C
ATOM 49 O3' DG A 3 39.305 29.611 -6.694 1.00 13.11 O
ATOM 50 C2' DG A 3 38.964 28.594 -4.531 1.00 13.65 C
ATOM 51 C1' DG A 3 39.829 28.582 -3.266 1.00 12.41 C
ATOM 52 N9 DG A 3 39.228 29.331 -2.166 1.00 12.12 N
ATOM 53 C8 DG A 3 39.594 30.554 -1.663 1.00 11.58 C
ATOM 54 N7 DG A 3 38.862 30.953 -0.663 1.00 11.79 N
ATOM 55 C5 DG A 3 37.940 29.923 -0.492 1.00 11.50 C
ATOM 56 C6 DG A 3 36.881 29.778 0.443 1.00 11.16 C
ATOM 57 O6 DG A 3 36.547 30.567 1.339 1.00 11.58 O
ATOM 58 N1 DG A 3 36.182 28.579 0.259 1.00 12.09 N
ATOM 59 C2 DG A 3 36.476 27.629 -0.698 1.00 11.36 C
ATOM 60 N2 DG A 3 35.704 26.537 -0.733 1.00 10.88 N
ATOM 61 N3 DG A 3 37.472 27.754 -1.570 1.00 10.50 N
ATOM 62 C4 DG A 3 38.154 28.919 -1.410 1.00 11.69 C
HETATM 63 N1 TTI A 4 34.521 28.495 -3.603 1.00 11.65 N
HETATM 64 C2 TTI A 4 33.623 28.588 -2.562 1.00 11.82 C
HETATM 65 O2 TTI A 4 32.779 27.760 -2.332 1.00 11.40 O
HETATM 66 N3 TTI A 4 33.717 29.711 -1.797 1.00 11.10 N
HETATM 67 C4 TTI A 4 34.616 30.745 -1.961 1.00 12.15 C
HETATM 68 O4 TTI A 4 34.625 31.724 -1.210 1.00 10.76 O
HETATM 69 C5 TTI A 4 35.530 30.592 -3.073 1.00 10.78 C
HETATM 70 C6 TTI A 4 35.459 29.488 -3.830 1.00 12.57 C
HETATM 71 C1' TTI A 4 34.496 27.280 -4.480 1.00 12.38 C
HETATM 72 C2' TTI A 4 33.422 27.295 -5.569 1.00 11.05 C
HETATM 73 C3' TTI A 4 34.224 27.804 -6.763 1.00 11.78 C
HETATM 74 O3' TTI A 4 33.689 27.381 -8.001 1.00 12.21 O
HETATM 75 C4' TTI A 4 35.579 27.140 -6.548 1.00 12.65 C
HETATM 76 O4' TTI A 4 35.760 27.188 -5.110 1.00 12.44 O
HETATM 77 C5' TTI A 4 36.742 27.826 -7.244 1.00 12.89 C
HETATM 78 O5' TTI A 4 36.811 29.199 -6.839 1.00 12.90 O
HETATM 79 P TTI A 4 37.969 30.189 -7.349 1.00 12.84 P
HETATM 80 O1P TTI A 4 37.711 31.513 -6.756 1.00 14.57 O
HETATM 81 O2P TTI A 4 38.112 30.073 -8.809 1.00 13.15 O
HETATM 82 TE5 TTI A 4 36.982 32.030 -3.455 0.75 15.87 TE
ATOM 83 P DA A 5 32.535 28.217 -8.715 1.00 15.49 P
ATOM 84 OP1 DA A 5 32.403 27.659 -10.080 1.00 16.09 O
ATOM 85 OP2 DA A 5 32.739 29.665 -8.500 1.00 17.06 O
ATOM 86 O5' DA A 5 31.257 27.801 -7.854 1.00 13.84 O
ATOM 87 C5' DA A 5 30.184 28.669 -7.634 1.00 14.52 C
ATOM 88 C4' DA A 5 29.365 28.123 -6.479 1.00 13.13 C
ATOM 89 O4' DA A 5 30.201 28.026 -5.298 1.00 13.55 O
ATOM 90 C3' DA A 5 28.214 29.025 -6.086 1.00 12.73 C
ATOM 91 O3' DA A 5 27.083 28.630 -6.823 1.00 13.54 O
ATOM 92 C2' DA A 5 28.036 28.724 -4.599 1.00 12.49 C
ATOM 93 C1' DA A 5 29.490 28.540 -4.184 1.00 12.14 C
ATOM 94 N9 DA A 5 30.171 29.753 -3.731 1.00 12.21 N
ATOM 95 C8 DA A 5 31.219 30.384 -4.344 1.00 12.10 C
ATOM 96 N7 DA A 5 31.659 31.430 -3.689 1.00 12.08 N
ATOM 97 C5 DA A 5 30.849 31.487 -2.567 1.00 11.76 C
ATOM 98 C6 DA A 5 30.807 32.367 -1.467 1.00 12.21 C
ATOM 99 N6 DA A 5 31.630 33.394 -1.330 1.00 12.00 N
ATOM 100 N1 DA A 5 29.868 32.150 -0.515 1.00 12.35 N
ATOM 101 C2 DA A 5 29.041 31.105 -0.657 1.00 11.72 C
ATOM 102 N3 DA A 5 28.997 30.207 -1.637 1.00 11.36 N
ATOM 103 C4 DA A 5 29.928 30.455 -2.572 1.00 12.05 C
ATOM 104 P DC A 6 26.064 29.729 -7.342 1.00 14.47 P
ATOM 105 OP1 DC A 6 24.985 29.010 -8.065 1.00 14.24 O
ATOM 106 OP2 DC A 6 26.837 30.819 -7.973 1.00 14.15 O
ATOM 107 O5' DC A 6 25.421 30.286 -5.991 1.00 14.84 O
ATOM 108 C5' DC A 6 24.487 29.513 -5.246 1.00 13.67 C
ATOM 109 C4' DC A 6 24.194 30.216 -3.942 1.00 13.22 C
ATOM 110 O4' DC A 6 25.406 30.331 -3.152 1.00 14.01 O
ATOM 111 C3' DC A 6 23.757 31.663 -4.117 1.00 13.49 C
ATOM 112 O3' DC A 6 22.399 31.713 -4.504 1.00 15.16 O
ATOM 113 C2' DC A 6 23.973 32.177 -2.705 1.00 14.63 C
ATOM 114 C1' DC A 6 25.331 31.543 -2.429 1.00 13.23 C
ATOM 115 N1 DC A 6 26.493 32.416 -2.791 1.00 12.99 N
ATOM 116 C2 DC A 6 26.856 33.430 -1.885 1.00 13.77 C
ATOM 117 O2 DC A 6 26.205 33.560 -0.848 1.00 14.02 O
ATOM 118 N3 DC A 6 27.920 34.223 -2.158 1.00 12.45 N
ATOM 119 C4 DC A 6 28.614 34.052 -3.281 1.00 12.78 C
ATOM 120 N4 DC A 6 29.650 34.870 -3.483 1.00 13.15 N
ATOM 121 C5 DC A 6 28.256 33.036 -4.234 1.00 12.99 C
ATOM 122 C6 DC A 6 27.200 32.250 -3.956 1.00 13.35 C
ATOM 123 P DA A 7 21.810 33.009 -5.242 1.00 15.78 P
ATOM 124 OP1 DA A 7 20.462 32.658 -5.764 1.00 17.09 O
ATOM 125 OP2 DA A 7 22.830 33.543 -6.182 1.00 15.68 O
ATOM 126 O5' DA A 7 21.638 34.033 -4.037 1.00 15.64 O
ATOM 127 C5' DA A 7 20.770 33.802 -2.942 1.00 15.33 C
ATOM 128 C4' DA A 7 20.872 35.015 -2.034 1.00 13.92 C
ATOM 129 O4' DA A 7 22.199 35.100 -1.466 1.00 14.54 O
ATOM 130 C3' DA A 7 20.720 36.354 -2.722 1.00 13.69 C
ATOM 131 O3' DA A 7 19.344 36.650 -2.783 1.00 15.60 O
ATOM 132 C2' DA A 7 21.464 37.331 -1.822 1.00 13.78 C
ATOM 133 C1' DA A 7 22.603 36.457 -1.352 1.00 13.49 C
ATOM 134 N9 DA A 7 23.868 36.593 -2.069 1.00 12.97 N
ATOM 135 C8 DA A 7 24.318 35.844 -3.119 1.00 12.83 C
ATOM 136 N7 DA A 7 25.518 36.181 -3.527 1.00 12.89 N
ATOM 137 C5 DA A 7 25.896 37.210 -2.677 1.00 13.21 C
ATOM 138 C6 DA A 7 27.076 37.996 -2.570 1.00 12.64 C
ATOM 139 N6 DA A 7 28.144 37.851 -3.372 1.00 12.83 N
ATOM 140 N1 DA A 7 27.111 38.950 -1.603 1.00 12.77 N
ATOM 141 C2 DA A 7 26.046 39.092 -0.796 1.00 12.88 C
ATOM 142 N3 DA A 7 24.900 38.410 -0.809 1.00 12.77 N
ATOM 143 C4 DA A 7 24.885 37.474 -1.768 1.00 12.62 C
ATOM 144 P DC A 8 18.792 37.625 -3.896 1.00 15.71 P
ATOM 145 OP1 DC A 8 17.333 37.632 -3.690 1.00 16.27 O
ATOM 146 OP2 DC A 8 19.320 37.184 -5.202 1.00 17.41 O
ATOM 147 O5' DC A 8 19.376 39.070 -3.561 1.00 15.47 O
ATOM 148 C5' DC A 8 18.866 39.745 -2.430 1.00 15.45 C
ATOM 149 C4' DC A 8 19.597 41.039 -2.162 1.00 17.10 C
ATOM 150 O4' DC A 8 21.008 40.747 -2.062 1.00 16.52 O
ATOM 151 C3' DC A 8 19.412 42.103 -3.239 1.00 18.18 C
ATOM 152 O3' DC A 8 19.171 43.348 -2.618 1.00 21.35 O
ATOM 153 C2' DC A 8 20.737 42.123 -3.977 1.00 17.37 C
ATOM 154 C1' DC A 8 21.714 41.626 -2.911 1.00 16.17 C
ATOM 155 N1 DC A 8 22.888 40.956 -3.549 1.00 15.41 N
ATOM 156 C2 DC A 8 24.172 41.490 -3.338 1.00 14.51 C
ATOM 157 O2 DC A 8 24.307 42.478 -2.593 1.00 14.62 O
ATOM 158 N3 DC A 8 25.229 40.900 -3.957 1.00 14.63 N
ATOM 159 C4 DC A 8 25.046 39.829 -4.747 1.00 14.28 C
ATOM 160 N4 DC A 8 26.113 39.289 -5.331 1.00 13.66 N
ATOM 161 C5 DC A 8 23.751 39.271 -4.970 1.00 12.96 C
ATOM 162 C6 DC A 8 22.717 39.866 -4.369 1.00 14.39 C
TER 163 DC A 8
HETATM 164 MG MG A 9 32.508 37.550 -1.471 1.00 12.21 MG
HETATM 165 O HOH A 10 42.712 25.200 -0.002 1.00 21.21 O
HETATM 166 O HOH A 11 23.019 36.116 -7.159 1.00 26.34 O
HETATM 167 O HOH A 12 41.579 34.640 0.024 1.00 22.46 O
HETATM 168 O HOH A 13 20.077 29.516 -2.478 1.00 32.52 O
HETATM 169 O HOH A 14 46.234 36.141 -2.515 1.00 22.36 O
HETATM 170 O HOH A 15 47.554 39.377 -1.107 1.00 23.27 O
HETATM 171 O HOH A 16 48.132 35.486 -4.031 1.00 28.15 O
HETATM 172 O HOH A 17 26.988 35.558 -5.834 1.00 25.89 O
HETATM 173 O HOH A 18 27.430 27.792 -1.337 1.00 10.11 O
HETATM 174 O HOH A 19 35.564 36.986 -0.824 1.00 27.55 O
HETATM 175 O HOH A 20 29.977 38.739 -6.023 1.00 25.80 O
HETATM 176 O HOH A 21 43.186 36.328 3.613 1.00 26.28 O
HETATM 177 O HOH A 22 31.087 34.605 -6.117 1.00 27.67 O
HETATM 178 O HOH A 23 38.138 32.496 -10.433 1.00 46.38 O
HETATM 179 O HOH A 24 18.438 34.701 -6.020 1.00 33.73 O
HETATM 180 O HOH A 25 33.400 38.945 -0.632 1.00 19.47 O
HETATM 181 O HOH A 26 34.287 40.287 -3.918 1.00 38.32 O
HETATM 182 O HOH A 27 30.363 26.317 -11.171 1.00 26.77 O
HETATM 183 O HOH A 28 35.092 32.798 -6.590 1.00 28.54 O
HETATM 184 O HOH A 29 27.949 29.760 -10.459 1.00 28.51 O
HETATM 185 O HOH A 30 27.616 33.627 -7.603 1.00 31.80 O
HETATM 186 O HOH A 31 19.189 30.872 -4.536 1.00 32.00 O
HETATM 187 O HOH A 32 29.962 32.367 -7.139 1.00 40.53 O
HETATM 188 O HOH A 33 28.876 34.730 -9.779 1.00 38.44 O
HETATM 189 O HOH A 34 28.463 37.389 -9.738 1.00 36.52 O
HETATM 190 O HOH A 35 38.591 33.770 -3.309 1.00 27.20 O
HETATM 191 O HOH A 36 41.368 33.232 -2.090 1.00 22.06 O
HETATM 192 O HOH A 37 32.524 37.864 -3.333 1.00 2.00 O
HETATM 193 O HOH A 38 22.595 39.758 0.293 1.00 16.47 O
HETATM 194 O HOH A 39 37.828 25.635 -3.414 1.00 16.80 O
HETATM 195 O HOH A 40 46.848 37.925 0.926 1.00 15.11 O
HETATM 196 O HOH A 41 16.695 42.285 -1.113 1.00 20.66 O
HETATM 197 O HOH A 42 25.228 26.695 -2.550 1.00 15.02 O
HETATM 198 O HOH A 43 25.474 37.272 -7.269 1.00 16.01 O
HETATM 199 O HOH A 44 22.656 27.851 -1.979 1.00 16.08 O
HETATM 200 O HOH A 45 33.390 33.402 -4.569 1.00 22.25 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 49 79
CONECT 63 64 70 71
CONECT 64 63 65 66
CONECT 65 64
CONECT 66 64 67
CONECT 67 66 68 69
CONECT 68 67
CONECT 69 67 70 82
CONECT 70 63 69
CONECT 71 63 72 76
CONECT 72 71 73
CONECT 73 72 74 75
CONECT 74 73 83
CONECT 75 73 76 77
CONECT 76 71 75
CONECT 77 75 78
CONECT 78 77 79
CONECT 79 49 78 80 81
CONECT 80 79
CONECT 81 79
CONECT 82 69 190
CONECT 83 74
CONECT 164 180 192
CONECT 180 164
CONECT 190 82
CONECT 192 164
MASTER 344 0 3 0 0 0 1 6 199 1 49 1
END