HEADER TRANSFERASE/DNA 18-NOV-14 4RU9
TITLE CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING DCMPNPP
TITLE 2 OPPOSITE A MEFAPY-DG ADDUCTED DNA TEMPLATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE ETA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 1-432;
COMPND 5 SYNONYM: RAD30 HOMOLOG A, XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN;
COMPND 6 EC: 2.7.7.7;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: NUCLEIC ACIDS TEMPLATE: CAT(MF7)ATGACGCT;
COMPND 10 CHAIN: T;
COMPND 11 ENGINEERED: YES;
COMPND 12 MOL_ID: 3;
COMPND 13 MOLECULE: NUCLEIC ACIDS PRIMAR: AGCGTCAT;
COMPND 14 CHAIN: P;
COMPND 15 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: POLH, RAD30, RAD30A, XPV;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 11 ORGANISM_TAXID: 32630;
SOURCE 12 OTHER_DETAILS: CHEMICALLY SYNTHESIZED;
SOURCE 13 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES;
SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 16 ORGANISM_TAXID: 32630;
SOURCE 17 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA DAMAGE, DNA-DIRECTED DNA POLYMERASE, CYTIDINE TRIPHOSPHATE, Y-
KEYWDS 2 FAMILY POLYMERASE, TRANS-LESION SYNTHESIS (TLS), DNA BINDING,
KEYWDS 3 MEFAPY-DG LESION BYPASS, 2, 6-DIAMINO-4-HYDROXY-N(5)-(METHYL)-
KEYWDS 4 FORMAMIDOPYRIMIDINE (MEFAPY-DG) LESION, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.PATRA,M.EGLI
REVDAT 2 20-SEP-23 4RU9 1 REMARK LINK
REVDAT 1 05-AUG-15 4RU9 0
JRNL AUTH A.PATRA,S.BANERJEE,T.L.JOHNSON SALYARD,C.K.MALIK,
JRNL AUTH 2 P.P.CHRISTOV,C.J.RIZZO,M.P.STONE,M.EGLI
JRNL TITL STRUCTURAL BASIS FOR ERROR-FREE BYPASS OF THE
JRNL TITL 2 5-N-METHYLFORMAMIDOPYRIMIDINE-DG LESION BY HUMAN DNA
JRNL TITL 3 POLYMERASE ETA AND SULFOLOBUS SOLFATARICUS P2 POLYMERASE IV.
JRNL REF J.AM.CHEM.SOC. V. 137 7011 2015
JRNL REFN ISSN 0002-7863
JRNL PMID 25988947
JRNL DOI 10.1021/JACS.5B02701
REMARK 2
REMARK 2 RESOLUTION. 2.65 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0073
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) : 2.65
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 3 NUMBER OF REFLECTIONS : 12503
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) : 0.162
REMARK 3 R VALUE (WORKING SET) : 0.159
REMARK 3 FREE R VALUE : 0.229
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200
REMARK 3 FREE R VALUE TEST SET COUNT : 688
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) : 2.65
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72
REMARK 3 REFLECTION IN BIN (WORKING SET) : 934
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80
REMARK 3 BIN R VALUE (WORKING SET) : 0.2210
REMARK 3 BIN FREE R VALUE SET COUNT : 46
REMARK 3 BIN FREE R VALUE : 0.3410
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3345
REMARK 3 NUCLEIC ACID ATOMS : 391
REMARK 3 HETEROGEN ATOMS : 30
REMARK 3 SOLVENT ATOMS : 138
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.75
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.16000
REMARK 3 B22 (A**2) : -0.16000
REMARK 3 B33 (A**2) : 0.52000
REMARK 3 B12 (A**2) : -0.08000
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): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.347
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.255
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.338
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3880 ; 0.011 ; 0.018
REMARK 3 BOND LENGTHS OTHERS (A): 3566 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5318 ; 1.512 ; 1.883
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8218 ; 1.408 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 429 ; 6.353 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;37.059 ;24.013
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 632 ;16.922 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;20.054 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 579 ; 0.086 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4100 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 877 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
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): 1713 ; 3.012 ; 4.508
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1712 ; 3.011 ; 4.506
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2140 ; 4.787 ; 6.745
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2141 ; 4.739 ; 6.797
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2167 ; 3.502 ; 5.088
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2168 ; 3.569 ; 5.123
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3178 ; 5.684 ; 7.566
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 16437 ; 9.870 ;44.011
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 16392 ; 9.868 ;44.009
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 : NULL
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 4RU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-14.
REMARK 100 THE DEPOSITION ID IS D_1000087803.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-AUG-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-D
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.07810
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16058
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : 5.500
REMARK 200 R MERGE (I) : 0.14500
REMARK 200 R SYM (I) : 0.14500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7810
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 4.30
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.026
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER (MR)
REMARK 200 STARTING MODEL: PDB ENTRY 4O3N
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.37
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5.5, 5MM MAGNESIUM
REMARK 280 CHLORIDE, 25% PEG 2000 MME , VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 291.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+5/6
REMARK 290 6555 X-Y,X,Z+1/6
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.20800
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.41600
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.81200
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.02000
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.60400
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4310 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21870 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 THR A 155
REMARK 465 THR A 156
REMARK 465 ALA A 157
REMARK 465 GLU A 158
REMARK 465 GLU A 159
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 DC T 1 O5' C5' C4' O4' C3' C2' C1'
REMARK 470 DC T 1 N1 C2 O2 N3 C4 N4 C5
REMARK 470 DC T 1 C6
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OG1 THR A 3 OE1 GLN A 5 1.95
REMARK 500
REMARK 500 REMARK: NULL
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 MF7 T 4 C3' - O3' - P ANGL. DEV. = -8.3 DEGREES
REMARK 500 DA T 5 O3' - P - OP2 ANGL. DEV. = 15.9 DEGREES
REMARK 500 DA T 5 O3' - P - OP1 ANGL. DEV. = -25.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 THR A 3 40.14 21.00
REMARK 500 CYS A 16 65.91 25.89
REMARK 500 TYR A 39 86.53 64.47
REMARK 500 SER A 62 45.60 71.03
REMARK 500 SER A 217 -158.55 -157.85
REMARK 500 SER A 257 -2.96 78.71
REMARK 500 ALA A 332 26.84 -142.06
REMARK 500 ASP A 375 144.74 -36.94
REMARK 500 LEU A 378 -80.27 -8.54
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 502 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD2
REMARK 620 2 MET A 14 O 76.0
REMARK 620 3 ASP A 115 OD2 91.8 84.5
REMARK 620 4 0KX A 501 O1B 161.8 87.8 95.1
REMARK 620 5 0KX A 501 O1A 106.2 175.8 98.9 89.4
REMARK 620 6 0KX A 501 O3G 87.6 92.4 176.9 84.7 84.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 503 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD1
REMARK 620 2 ASP A 115 OD1 87.3
REMARK 620 3 GLU A 116 OE2 75.5 84.3
REMARK 620 4 0KX A 501 O1A 98.8 105.1 169.0
REMARK 620 5 HOH A 617 O 78.7 162.6 82.3 87.3
REMARK 620 6 DT P 8 O3' 153.9 83.9 79.2 107.2 104.3
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0KX A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 503
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4RUA RELATED DB: PDB
DBREF 4RU9 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432
DBREF 4RU9 T 1 12 PDB 4RU9 4RU9 1 12
DBREF 4RU9 P 1 8 PDB 4RU9 4RU9 1 8
SEQRES 1 A 432 MET ALA THR GLY GLN ASP ARG VAL VAL ALA LEU VAL ASP
SEQRES 2 A 432 MET ASP CYS PHE PHE VAL GLN VAL GLU GLN ARG GLN ASN
SEQRES 3 A 432 PRO HIS LEU ARG ASN LYS PRO CYS ALA VAL VAL GLN TYR
SEQRES 4 A 432 LYS SER TRP LYS GLY GLY GLY ILE ILE ALA VAL SER TYR
SEQRES 5 A 432 GLU ALA ARG ALA PHE GLY VAL THR ARG SER MET TRP ALA
SEQRES 6 A 432 ASP ASP ALA LYS LYS LEU CYS PRO ASP LEU LEU LEU ALA
SEQRES 7 A 432 GLN VAL ARG GLU SER ARG GLY LYS ALA ASN LEU THR LYS
SEQRES 8 A 432 TYR ARG GLU ALA SER VAL GLU VAL MET GLU ILE MET SER
SEQRES 9 A 432 ARG PHE ALA VAL ILE GLU ARG ALA SER ILE ASP GLU ALA
SEQRES 10 A 432 TYR VAL ASP LEU THR SER ALA VAL GLN GLU ARG LEU GLN
SEQRES 11 A 432 LYS LEU GLN GLY GLN PRO ILE SER ALA ASP LEU LEU PRO
SEQRES 12 A 432 SER THR TYR ILE GLU GLY LEU PRO GLN GLY PRO THR THR
SEQRES 13 A 432 ALA GLU GLU THR VAL GLN LYS GLU GLY MET ARG LYS GLN
SEQRES 14 A 432 GLY LEU PHE GLN TRP LEU ASP SER LEU GLN ILE ASP ASN
SEQRES 15 A 432 LEU THR SER PRO ASP LEU GLN LEU THR VAL GLY ALA VAL
SEQRES 16 A 432 ILE VAL GLU GLU MET ARG ALA ALA ILE GLU ARG GLU THR
SEQRES 17 A 432 GLY PHE GLN CYS SER ALA GLY ILE SER HIS ASN LYS VAL
SEQRES 18 A 432 LEU ALA LYS LEU ALA CYS GLY LEU ASN LYS PRO ASN ARG
SEQRES 19 A 432 GLN THR LEU VAL SER HIS GLY SER VAL PRO GLN LEU PHE
SEQRES 20 A 432 SER GLN MET PRO ILE ARG LYS ILE ARG SER LEU GLY GLY
SEQRES 21 A 432 LYS LEU GLY ALA SER VAL ILE GLU ILE LEU GLY ILE GLU
SEQRES 22 A 432 TYR MET GLY GLU LEU THR GLN PHE THR GLU SER GLN LEU
SEQRES 23 A 432 GLN SER HIS PHE GLY GLU LYS ASN GLY SER TRP LEU TYR
SEQRES 24 A 432 ALA MET CYS ARG GLY ILE GLU HIS ASP PRO VAL LYS PRO
SEQRES 25 A 432 ARG GLN LEU PRO LYS THR ILE GLY CYS SER LYS ASN PHE
SEQRES 26 A 432 PRO GLY LYS THR ALA LEU ALA THR ARG GLU GLN VAL GLN
SEQRES 27 A 432 TRP TRP LEU LEU GLN LEU ALA GLN GLU LEU GLU GLU ARG
SEQRES 28 A 432 LEU THR LYS ASP ARG ASN ASP ASN ASP ARG VAL ALA THR
SEQRES 29 A 432 GLN LEU VAL VAL SER ILE ARG VAL GLN GLY ASP LYS ARG
SEQRES 30 A 432 LEU SER SER LEU ARG ARG CYS CYS ALA LEU THR ARG TYR
SEQRES 31 A 432 ASP ALA HIS LYS MET SER HIS ASP ALA PHE THR VAL ILE
SEQRES 32 A 432 LYS ASN CYS ASN THR SER GLY ILE GLN THR GLU TRP SER
SEQRES 33 A 432 PRO PRO LEU THR MET LEU PHE LEU CYS ALA THR LYS PHE
SEQRES 34 A 432 SER ALA SER
SEQRES 1 T 12 DC DA DT MF7 DA DT DG DA DC DG DC DT
SEQRES 1 P 8 DA DG DC DG DT DC DA DT
HET MF7 T 4 24
HET 0KX A 501 28
HET MG A 502 1
HET MG A 503 1
HETNAM MF7 N-{2-AMINO-5-[FORMYL(METHYL)AMINO]-6-HYDROXYPYRIMIDIN-
HETNAM 2 MF7 4-YL}-2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-
HETNAM 3 MF7 PENTOFURANOSYLAMINE
HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
HETNAM MG MAGNESIUM ION
FORMUL 2 MF7 C11 H18 N5 O8 P
FORMUL 4 0KX C9 H17 N4 O12 P3
FORMUL 5 MG 2(MG 2+)
FORMUL 7 HOH *138(H2 O)
HELIX 1 1 CYS A 16 ASN A 26 1 11
HELIX 2 2 PRO A 27 ARG A 30 5 4
HELIX 3 3 SER A 51 ALA A 56 1 6
HELIX 4 4 TRP A 64 CYS A 72 1 9
HELIX 5 5 LEU A 89 ARG A 105 1 17
HELIX 6 6 LEU A 121 LYS A 131 1 11
HELIX 7 7 SER A 138 LEU A 142 5 5
HELIX 8 8 GLN A 162 LEU A 178 1 17
HELIX 9 9 SER A 185 GLY A 209 1 25
HELIX 10 10 ASN A 219 ASN A 230 1 12
HELIX 11 11 SER A 239 GLY A 241 5 3
HELIX 12 12 SER A 242 SER A 248 1 7
HELIX 13 13 GLN A 249 MET A 250 5 2
HELIX 14 14 PRO A 251 ILE A 255 5 5
HELIX 15 15 GLY A 260 GLY A 271 1 12
HELIX 16 16 TYR A 274 PHE A 281 5 8
HELIX 17 17 THR A 282 GLY A 291 1 10
HELIX 18 18 GLY A 291 CYS A 302 1 12
HELIX 19 19 PRO A 326 ALA A 330 5 5
HELIX 20 20 ARG A 334 ASP A 360 1 27
HELIX 21 21 ASP A 391 VAL A 402 1 12
HELIX 22 22 ILE A 403 ASN A 407 5 5
SHEET 1 A 6 ILE A 109 ARG A 111 0
SHEET 2 A 6 GLU A 116 ASP A 120 -1 O TYR A 118 N GLU A 110
SHEET 3 A 6 VAL A 9 MET A 14 -1 N ALA A 10 O VAL A 119
SHEET 4 A 6 CYS A 212 SER A 217 -1 O SER A 213 N ASP A 13
SHEET 5 A 6 GLN A 235 LEU A 237 1 O THR A 236 N ALA A 214
SHEET 6 A 6 THR A 145 ILE A 147 1 N TYR A 146 O GLN A 235
SHEET 1 B 3 GLY A 46 VAL A 50 0
SHEET 2 B 3 CYS A 34 GLN A 38 -1 N VAL A 36 O ALA A 49
SHEET 3 B 3 LEU A 76 GLN A 79 1 O ALA A 78 N VAL A 37
SHEET 1 C 2 GLU A 82 SER A 83 0
SHEET 2 C 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83
SHEET 1 D 3 ILE A 319 ASN A 324 0
SHEET 2 D 3 GLU A 414 THR A 427 -1 O ALA A 426 N ILE A 319
SHEET 3 D 3 LEU A 331 THR A 333 -1 N LEU A 331 O LEU A 419
SHEET 1 E 4 ILE A 319 ASN A 324 0
SHEET 2 E 4 GLU A 414 THR A 427 -1 O ALA A 426 N ILE A 319
SHEET 3 E 4 GLN A 365 VAL A 372 -1 N VAL A 367 O CYS A 425
SHEET 4 E 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368
SHEET 1 F 2 ARG A 361 VAL A 362 0
SHEET 2 F 2 SER A 430 ALA A 431 -1 O SER A 430 N VAL A 362
LINK O3' DT T 3 P1 MF7 T 4 1555 1555 1.71
LINK O3' MF7 T 4 P DA T 5 1555 1555 1.59
LINK OD2 ASP A 13 MG MG A 502 1555 1555 1.87
LINK OD1 ASP A 13 MG MG A 503 1555 1555 2.07
LINK O MET A 14 MG MG A 502 1555 1555 2.20
LINK OD2 ASP A 115 MG MG A 502 1555 1555 2.05
LINK OD1 ASP A 115 MG MG A 503 1555 1555 2.19
LINK OE2 GLU A 116 MG MG A 503 1555 1555 2.22
LINK O1B 0KX A 501 MG MG A 502 1555 1555 1.89
LINK O1A 0KX A 501 MG MG A 502 1555 1555 2.13
LINK O3G 0KX A 501 MG MG A 502 1555 1555 2.17
LINK O1A 0KX A 501 MG MG A 503 1555 1555 1.97
LINK MG MG A 503 O HOH A 617 1555 1555 2.28
LINK MG MG A 503 O3' DT P 8 1555 1555 2.33
CISPEP 1 LEU A 150 PRO A 151 0 0.98
CISPEP 2 LYS A 231 PRO A 232 0 4.78
CISPEP 3 SER A 416 PRO A 417 0 -3.13
SITE 1 AC1 21 ASP A 13 MET A 14 ASP A 15 CYS A 16
SITE 2 AC1 21 PHE A 17 PHE A 18 ILE A 48 ALA A 49
SITE 3 AC1 21 TYR A 52 ARG A 55 ARG A 61 ASP A 115
SITE 4 AC1 21 LYS A 231 MG A 502 MG A 503 HOH A 617
SITE 5 AC1 21 HOH A 626 HOH A 663 HOH A 695 DT P 8
SITE 6 AC1 21 MF7 T 4
SITE 1 AC2 5 ASP A 13 MET A 14 ASP A 115 0KX A 501
SITE 2 AC2 5 MG A 503
SITE 1 AC3 7 ASP A 13 ASP A 115 GLU A 116 0KX A 501
SITE 2 AC3 7 MG A 502 HOH A 617 DT P 8
CRYST1 98.971 98.971 81.624 90.00 90.00 120.00 P 61 6
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 0.010104 0.005834 0.000000 0.00000
SCALE2 0.000000 0.011667 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012251 0.00000