HEADER TRANSFERASE/DNA 18-DEC-13 4O3S TITLE CRYSTAL STRUCTURE OF HUMAN POLYMERASE ETA EXTENDING AN 8-OXOG DNA TITLE 2 LESION: POST INSERTION OF 8-OXOG-DC PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE ETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RAD30 HOMOLOG A, XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*AP*TP*GP*(8OG)P*TP*GP*AP*CP*GP*CP*T)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: NUCLEIC ACIDS TEMPLATE: CAT G(8OG)T GAC GCT; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*C)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: NUCLEIC ACIDS PRIMAR: AGCGTCAC 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 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS CATALYTIC DOMAIN, DNA, DNA DAMAGE, DNA-DIRECTED DNA POLYMERASE, KEYWDS 2 CYTOSINE TRIPHOSPHATE, Y-FAMILY POLYMERASE, TRANS-LESION SYNTHESIS KEYWDS 3 (TLS), DNA BINDING, 8-OXOG LESION BYPASS, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PATRA,M.EGLI REVDAT 3 20-SEP-23 4O3S 1 REMARK LINK REVDAT 2 02-JUL-14 4O3S 1 JRNL REVDAT 1 30-APR-14 4O3S 0 JRNL AUTH A.PATRA,L.D.NAGY,Q.ZHANG,Y.SU,L.MULLER,F.P.GUENGERICH,M.EGLI JRNL TITL KINETICS, STRUCTURE, AND MECHANISM OF JRNL TITL 2 8-OXO-7,8-DIHYDRO-2'-DEOXYGUANOSINE BYPASS BY HUMAN DNA JRNL TITL 3 POLYMERASE ETA JRNL REF J.BIOL.CHEM. V. 289 16867 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24759104 JRNL DOI 10.1074/JBC.M114.551820 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1551) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 47707 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2412 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.5834 - 4.4132 0.99 2701 158 0.1772 0.1997 REMARK 3 2 4.4132 - 3.5034 1.00 2687 150 0.1429 0.1810 REMARK 3 3 3.5034 - 3.0607 1.00 2687 140 0.1576 0.1903 REMARK 3 4 3.0607 - 2.7809 1.00 2689 129 0.1764 0.1980 REMARK 3 5 2.7809 - 2.5816 1.00 2670 154 0.1753 0.2237 REMARK 3 6 2.5816 - 2.4294 1.00 2679 136 0.1821 0.2099 REMARK 3 7 2.4294 - 2.3078 1.00 2677 139 0.1698 0.2214 REMARK 3 8 2.3078 - 2.2073 1.00 2660 136 0.1662 0.1929 REMARK 3 9 2.2073 - 2.1224 1.00 2649 156 0.1763 0.2072 REMARK 3 10 2.1224 - 2.0491 1.00 2655 120 0.1779 0.2329 REMARK 3 11 2.0491 - 1.9850 1.00 2672 139 0.1848 0.2785 REMARK 3 12 1.9850 - 1.9283 1.00 2665 130 0.1864 0.2171 REMARK 3 13 1.9283 - 1.8775 1.00 2656 152 0.1887 0.2569 REMARK 3 14 1.8775 - 1.8317 1.00 2619 144 0.1924 0.2536 REMARK 3 15 1.8317 - 1.7901 1.00 2652 155 0.2060 0.2905 REMARK 3 16 1.7901 - 1.7520 0.99 2648 144 0.2226 0.2603 REMARK 3 17 1.7520 - 1.7169 0.99 2629 130 0.2318 0.2988 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 3935 REMARK 3 ANGLE : 1.163 5412 REMARK 3 CHIRALITY : 0.046 606 REMARK 3 PLANARITY : 0.005 625 REMARK 3 DIHEDRAL : 19.679 1536 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4O3S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084005. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-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-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47707 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 31.2550 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.75700 REMARK 200 R SYM FOR SHELL (I) : 0.75700 REMARK 200 FOR SHELL : 2.622 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 4ECQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5.5, 5MM MAGNESIUM REMARK 280 CHLORIDE, 17% 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 27.19867 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 54.39733 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 40.79800 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 67.99667 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 13.59933 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: 5310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21370 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 O HOH A 683 O HOH A 962 2.04 REMARK 500 O HOH T 129 O HOH T 130 2.09 REMARK 500 O HOH A 964 O HOH A 991 2.10 REMARK 500 O HOH A 707 O HOH A 779 2.11 REMARK 500 O HOH A 674 O HOH A 828 2.12 REMARK 500 O HOH T 130 O HOH T 134 2.14 REMARK 500 O HOH A 898 O HOH A 990 2.15 REMARK 500 O HOH A 664 O HOH A 745 2.15 REMARK 500 O HOH A 901 O HOH A 978 2.15 REMARK 500 O HOH A 873 O HOH A 895 2.17 REMARK 500 O HOH A 903 O HOH T 128 2.18 REMARK 500 O HOH A 942 O HOH A 992 2.19 REMARK 500 O HOH A 727 O HOH A 787 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 889 O HOH T 133 5344 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT T 6 O3' DT T 6 C3' -0.046 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 DG T 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA P 7 O4' - C1' - N9 ANGL. DEV. = 1.8 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 CYS A 16 65.39 20.06 REMARK 500 TYR A 39 85.53 69.34 REMARK 500 GLN A 135 99.05 47.85 REMARK 500 SER A 217 -157.98 -155.37 REMARK 500 SER A 257 -10.29 93.82 REMARK 500 ASN A 407 93.42 -66.54 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 78.5 REMARK 620 3 ASP A 115 OD2 102.7 85.0 REMARK 620 4 0KX A 501 O1B 160.6 88.9 90.7 REMARK 620 5 0KX A 501 O2A 107.8 173.6 92.2 85.3 REMARK 620 6 0KX A 501 O1G 82.6 92.1 173.3 83.1 90.1 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 101.3 REMARK 620 3 GLU A 116 OE2 81.3 129.4 REMARK 620 4 0KX A 501 O2A 101.2 93.6 135.9 REMARK 620 5 HOH A 668 O 81.3 168.8 61.6 75.2 REMARK 620 6 DC P 8 O3' 169.5 84.1 88.3 87.4 95.2 REMARK 620 7 DC P 8 O3' 163.5 73.0 90.4 94.7 107.4 13.0 REMARK 620 N 1 2 3 4 5 6 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 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4O3N RELATED DB: PDB REMARK 900 RELATED ID: 4O3O RELATED DB: PDB REMARK 900 RELATED ID: 4O3P RELATED DB: PDB REMARK 900 RELATED ID: 4O3Q RELATED DB: PDB REMARK 900 RELATED ID: 4O3R RELATED DB: PDB DBREF 4O3S A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 4O3S T 1 12 PDB 4O3S 4O3S 1 12 DBREF 4O3S P 1 8 PDB 4O3S 4O3S 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 DG 8OG DT DG DA DC DG DC DT SEQRES 1 P 8 DA DG DC DG DT DC DA DC MODRES 4O3S 8OG T 5 DG HET 8OG T 5 23 HET 0KX A 501 28 HET MG A 502 1 HET MG A 503 1 HET GOL A 504 6 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 4 0KX C9 H17 N4 O12 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *452(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 ALA A 107 1 19 HELIX 6 6 LEU A 121 LEU A 132 1 12 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 242 GLN A 249 1 8 HELIX 12 12 MET A 250 ILE A 255 5 6 HELIX 13 13 GLY A 260 GLY A 271 1 12 HELIX 14 14 TYR A 274 PHE A 281 5 8 HELIX 15 15 THR A 282 GLY A 291 1 10 HELIX 16 16 GLY A 291 CYS A 302 1 12 HELIX 17 17 PRO A 326 ALA A 330 5 5 HELIX 18 18 ARG A 334 ASP A 360 1 27 HELIX 19 19 ASP A 391 LYS A 404 1 14 HELIX 20 20 ASN A 405 ASN A 407 5 3 SHEET 1 A 6 ILE A 109 SER A 113 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 VAL A 12 O ALA A 117 SHEET 4 A 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9 SHEET 5 A 6 GLN A 235 LEU A 237 1 O THR A 236 N ILE A 216 SHEET 6 A 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237 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 ILE A 48 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 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 D 3 LEU A 331 THR A 333 -1 N ALA A 332 O TRP A 415 SHEET 1 E 4 ILE A 319 ASN A 324 0 SHEET 2 E 4 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 E 4 ARG A 361 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 LINK O3' DG T 4 P 8OG T 5 1555 1555 1.61 LINK O3' 8OG T 5 P DT T 6 1555 1555 1.60 LINK OD2 ASP A 13 MG MG A 502 1555 1555 2.07 LINK OD1 ASP A 13 MG MG A 503 1555 1555 2.07 LINK O MET A 14 MG MG A 502 1555 1555 2.27 LINK OD2 ASP A 115 MG MG A 502 1555 1555 2.18 LINK OD1 ASP A 115 MG MG A 503 1555 1555 2.22 LINK OE2 GLU A 116 MG MG A 503 1555 1555 2.20 LINK O1B 0KX A 501 MG MG A 502 1555 1555 2.16 LINK O2A 0KX A 501 MG MG A 502 1555 1555 2.21 LINK O1G 0KX A 501 MG MG A 502 1555 1555 2.22 LINK O2A 0KX A 501 MG MG A 503 1555 1555 2.35 LINK MG MG A 503 O HOH A 668 1555 1555 2.29 LINK MG MG A 503 O3'B DC P 8 1555 1555 2.02 LINK MG MG A 503 O3'A DC P 8 1555 1555 2.68 CISPEP 1 LEU A 150 PRO A 151 0 1.14 CISPEP 2 LYS A 231 PRO A 232 0 1.01 CISPEP 3 SER A 416 PRO A 417 0 -4.78 SITE 1 AC1 27 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC1 27 PHE A 17 PHE A 18 ILE A 48 ALA A 49 SITE 3 AC1 27 TYR A 52 ARG A 55 ARG A 61 ASP A 115 SITE 4 AC1 27 LYS A 231 MG A 502 MG A 503 HOH A 617 SITE 5 AC1 27 HOH A 653 HOH A 668 HOH A 683 HOH A 704 SITE 6 AC1 27 HOH A 742 HOH A 942 HOH A 962 DC P 8 SITE 7 AC1 27 HOH P 105 DG T 4 8OG T 5 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 668 DC P 8 SITE 1 AC4 7 PRO A 244 PHE A 247 SER A 248 GLY A 276 SITE 2 AC4 7 GLU A 277 HOH A 603 HOH A 641 CRYST1 98.312 98.312 81.596 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 0.010172 0.005873 0.000000 0.00000 SCALE2 0.000000 0.011745 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012256 0.00000