HEADER TRANSFERASE/DNA 12-MAR-15 4YP3 TITLE MUTANT HUMAN DNA POLYMERASE ETA Q38A/R61A INSERTING DCTP OPPOSITE AN TITLE 2 8-OXOGUANINE LESION 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 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*TP*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'); 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 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS HUMAN DNA POLYMERASE ETA Q38A/R61A MUTATION 8-OXOGUANINE DCTP, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.SU,A.PATRA,J.M.HARP,M.EGLI,F.P.GUENGERICH REVDAT 6 27-SEP-23 4YP3 1 LINK REVDAT 5 04-DEC-19 4YP3 1 REMARK REVDAT 4 20-SEP-17 4YP3 1 SOURCE KEYWDS JRNL REMARK REVDAT 3 08-JUL-15 4YP3 1 JRNL REVDAT 2 20-MAY-15 4YP3 1 JRNL REVDAT 1 13-MAY-15 4YP3 0 JRNL AUTH Y.SU,A.PATRA,J.M.HARP,M.EGLI,F.P.GUENGERICH JRNL TITL ROLES OF RESIDUES ARG-61 AND GLN-38 OF HUMAN DNA POLYMERASE JRNL TITL 2 ETA IN BYPASS OF DEOXYGUANOSINE AND JRNL TITL 3 7,8-DIHYDRO-8-OXO-2'-DEOXYGUANOSINE. JRNL REF J.BIOL.CHEM. V. 290 15921 2015 JRNL REFN ESSN 1083-351X JRNL PMID 25947374 JRNL DOI 10.1074/JBC.M115.653691 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1839) 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 36405 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1875 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 42.7792 - 4.4412 0.99 2687 142 0.1868 0.2170 REMARK 3 2 4.4412 - 3.5256 1.00 2676 141 0.1402 0.1776 REMARK 3 3 3.5256 - 3.0801 1.00 2660 139 0.1506 0.2021 REMARK 3 4 3.0801 - 2.7986 1.00 2695 122 0.1655 0.1923 REMARK 3 5 2.7986 - 2.5980 1.00 2645 154 0.1651 0.2440 REMARK 3 6 2.5980 - 2.4448 1.00 2670 136 0.1743 0.2248 REMARK 3 7 2.4448 - 2.3224 1.00 2643 163 0.1646 0.2224 REMARK 3 8 2.3224 - 2.2213 1.00 2639 160 0.1648 0.2165 REMARK 3 9 2.2213 - 2.1358 1.00 2659 118 0.1707 0.2121 REMARK 3 10 2.1358 - 2.0621 1.00 2601 178 0.1756 0.2264 REMARK 3 11 2.0621 - 1.9976 1.00 2671 121 0.1936 0.2120 REMARK 3 12 1.9976 - 1.9405 1.00 2649 143 0.2061 0.2931 REMARK 3 13 1.9405 - 1.8894 1.00 2635 158 0.2452 0.3110 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.450 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 : 0.017 3745 REMARK 3 ANGLE : 1.644 5153 REMARK 3 CHIRALITY : 0.079 575 REMARK 3 PLANARITY : 0.007 602 REMARK 3 DIHEDRAL : 19.171 1413 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 4YP3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000206145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL 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 : 36455 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.79300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.211 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4O3P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NAMES (PH 6.0), POLYETHYLENE GLYCOL REMARK 280 MONOMETHYL ETHER 2000, AND CALCIUM CHLORIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K 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 27.32200 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 54.64400 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 40.98300 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 68.30500 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 13.66100 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: 5570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 GLY A 153 REMARK 465 PRO A 154 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 465 ASP A 375 REMARK 465 LYS A 376 REMARK 465 ARG A 377 REMARK 465 LEU A 378 REMARK 465 DC T 1 REMARK 465 DA T 2 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 MET A 1 CB CG SD CE REMARK 470 GLN A 130 CG CD OE1 NE2 REMARK 470 LYS A 131 CB CG CD CE NZ REMARK 470 LEU A 132 CG CD1 CD2 REMARK 470 GLN A 133 CB CG CD OE1 NE2 REMARK 470 GLN A 135 CB CG CD OE1 NE2 REMARK 470 GLN A 162 CB CG CD OE1 NE2 REMARK 470 LYS A 163 CG CD CE NZ REMARK 470 LYS A 168 CD CE NZ REMARK 470 GLN A 179 CG CD OE1 NE2 REMARK 470 ASP A 181 CG OD1 OD2 REMARK 470 ARG A 256 CZ NH1 NH2 REMARK 470 GLU A 268 CD OE1 OE2 REMARK 470 LYS A 293 CG CD CE NZ REMARK 470 LYS A 328 CB CG CD CE NZ REMARK 470 ALA A 332 CB REMARK 470 ARG A 334 CD NE CZ NH1 NH2 REMARK 470 GLU A 335 CD OE1 OE2 REMARK 470 VAL A 372 CG1 CG2 REMARK 470 GLN A 373 CG CD OE1 NE2 REMARK 470 GLY A 374 C O REMARK 470 SER A 380 CB OG REMARK 470 LEU A 381 CD2 REMARK 470 ARG A 382 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 405 CG OD1 ND2 REMARK 470 ILE A 411 CB CG1 CG2 CD1 REMARK 470 GLN A 412 CB CG CD OE1 NE2 REMARK 470 THR A 413 CB OG1 CG2 REMARK 470 SER A 416 CB OG REMARK 470 LYS A 428 CG CD CE NZ REMARK 470 DT T 3 P OP1 OP2 O5' C5' 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' -0.041 REMARK 500 DG P 2 O3' DG P 2 C3' -0.044 REMARK 500 DT P 8 O3' DT P 8 C3' -0.073 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 CYS A 321 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 DT T 3 C3' - C2' - C1' ANGL. DEV. = -7.0 DEGREES REMARK 500 DT T 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA T 5 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG T 10 O3' - P - OP2 ANGL. DEV. = 7.4 DEGREES REMARK 500 DG P 2 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 62.68 25.28 REMARK 500 TYR A 39 175.06 66.81 REMARK 500 LYS A 40 -24.47 -152.17 REMARK 500 SER A 62 28.21 47.74 REMARK 500 SER A 217 -158.42 -156.39 REMARK 500 SER A 257 -7.50 91.14 REMARK 500 SER A 380 -128.54 63.59 REMARK 500 ILE A 411 78.59 -115.76 REMARK 500 THR A 413 -8.88 75.00 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 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 ASP A 13 OD2 48.3 REMARK 620 3 MET A 14 O 105.2 79.3 REMARK 620 4 ASP A 115 OD2 80.3 118.5 86.0 REMARK 620 5 DCP A 501 O1A 82.5 114.0 166.1 83.8 REMARK 620 6 DCP A 501 O1B 158.3 153.3 88.0 83.5 81.4 REMARK 620 7 DCP A 501 O1G 110.2 78.3 104.3 162.1 83.3 82.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 ASP A 115 OD1 91.1 REMARK 620 3 GLU A 116 OE2 92.2 108.7 REMARK 620 4 DCP A 501 O1A 87.3 92.1 159.2 REMARK 620 5 HOH A 875 O 93.3 166.4 84.0 75.3 REMARK 620 6 DT P 8 O3' 169.1 78.2 89.9 94.5 97.5 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 DCP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA 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 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 DBREF 4YP3 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 4YP3 T 1 12 PDB 4YP3 4YP3 1 12 DBREF 4YP3 P 1 8 PDB 4YP3 4YP3 1 8 SEQADV 4YP3 GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 4YP3 PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 4YP3 HIS A 0 UNP Q9Y253 EXPRESSION TAG SEQADV 4YP3 ALA A 38 UNP Q9Y253 GLN 38 ENGINEERED MUTATION SEQADV 4YP3 ALA A 61 UNP Q9Y253 ARG 61 ENGINEERED MUTATION SEQRES 1 A 435 GLY PRO HIS MET ALA THR GLY GLN ASP ARG VAL VAL ALA SEQRES 2 A 435 LEU VAL ASP MET ASP CYS PHE PHE VAL GLN VAL GLU GLN SEQRES 3 A 435 ARG GLN ASN PRO HIS LEU ARG ASN LYS PRO CYS ALA VAL SEQRES 4 A 435 VAL ALA TYR LYS SER TRP LYS GLY GLY GLY ILE ILE ALA SEQRES 5 A 435 VAL SER TYR GLU ALA ARG ALA PHE GLY VAL THR ALA SER SEQRES 6 A 435 MET TRP ALA ASP ASP ALA LYS LYS LEU CYS PRO ASP LEU SEQRES 7 A 435 LEU LEU ALA GLN VAL ARG GLU SER ARG GLY LYS ALA ASN SEQRES 8 A 435 LEU THR LYS TYR ARG GLU ALA SER VAL GLU VAL MET GLU SEQRES 9 A 435 ILE MET SER ARG PHE ALA VAL ILE GLU ARG ALA SER ILE SEQRES 10 A 435 ASP GLU ALA TYR VAL ASP LEU THR SER ALA VAL GLN GLU SEQRES 11 A 435 ARG LEU GLN LYS LEU GLN GLY GLN PRO ILE SER ALA ASP SEQRES 12 A 435 LEU LEU PRO SER THR TYR ILE GLU GLY LEU PRO GLN GLY SEQRES 13 A 435 PRO THR THR ALA GLU GLU THR VAL GLN LYS GLU GLY MET SEQRES 14 A 435 ARG LYS GLN GLY LEU PHE GLN TRP LEU ASP SER LEU GLN SEQRES 15 A 435 ILE ASP ASN LEU THR SER PRO ASP LEU GLN LEU THR VAL SEQRES 16 A 435 GLY ALA VAL ILE VAL GLU GLU MET ARG ALA ALA ILE GLU SEQRES 17 A 435 ARG GLU THR GLY PHE GLN CYS SER ALA GLY ILE SER HIS SEQRES 18 A 435 ASN LYS VAL LEU ALA LYS LEU ALA CYS GLY LEU ASN LYS SEQRES 19 A 435 PRO ASN ARG GLN THR LEU VAL SER HIS GLY SER VAL PRO SEQRES 20 A 435 GLN LEU PHE SER GLN MET PRO ILE ARG LYS ILE ARG SER SEQRES 21 A 435 LEU GLY GLY LYS LEU GLY ALA SER VAL ILE GLU ILE LEU SEQRES 22 A 435 GLY ILE GLU TYR MET GLY GLU LEU THR GLN PHE THR GLU SEQRES 23 A 435 SER GLN LEU GLN SER HIS PHE GLY GLU LYS ASN GLY SER SEQRES 24 A 435 TRP LEU TYR ALA MET CYS ARG GLY ILE GLU HIS ASP PRO SEQRES 25 A 435 VAL LYS PRO ARG GLN LEU PRO LYS THR ILE GLY CYS SER SEQRES 26 A 435 LYS ASN PHE PRO GLY LYS THR ALA LEU ALA THR ARG GLU SEQRES 27 A 435 GLN VAL GLN TRP TRP LEU LEU GLN LEU ALA GLN GLU LEU SEQRES 28 A 435 GLU GLU ARG LEU THR LYS ASP ARG ASN ASP ASN ASP ARG SEQRES 29 A 435 VAL ALA THR GLN LEU VAL VAL SER ILE ARG VAL GLN GLY SEQRES 30 A 435 ASP LYS ARG LEU SER SER LEU ARG ARG CYS CYS ALA LEU SEQRES 31 A 435 THR ARG TYR ASP ALA HIS LYS MET SER HIS ASP ALA PHE SEQRES 32 A 435 THR VAL ILE LYS ASN CYS ASN THR SER GLY ILE GLN THR SEQRES 33 A 435 GLU TRP SER PRO PRO LEU THR MET LEU PHE LEU CYS ALA SEQRES 34 A 435 THR LYS PHE SER ALA SER SEQRES 1 T 12 DC DA DT 8OG DA DT DG DA DC DG DC DT SEQRES 1 P 8 DA DG DC DG DT DC DA DT HET 8OG T 4 23 HET DCP A 501 28 HET CA A 502 1 HET CA A 503 1 HET GOL A 504 6 HET GOL A 505 6 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM 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 DCP C9 H16 N3 O13 P3 FORMUL 5 CA 2(CA 2+) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 9 HOH *384(H2 O) HELIX 1 AA1 CYS A 16 ASN A 26 1 11 HELIX 2 AA2 PRO A 27 ARG A 30 5 4 HELIX 3 AA3 SER A 51 ALA A 56 1 6 HELIX 4 AA4 TRP A 64 CYS A 72 1 9 HELIX 5 AA5 LEU A 89 ALA A 107 1 19 HELIX 6 AA6 LEU A 121 LEU A 132 1 12 HELIX 7 AA7 SER A 138 LEU A 142 5 5 HELIX 8 AA8 GLN A 162 LEU A 178 1 17 HELIX 9 AA9 SER A 185 GLY A 209 1 25 HELIX 10 AB1 ASN A 219 ASN A 230 1 12 HELIX 11 AB2 SER A 239 GLY A 241 5 3 HELIX 12 AB3 SER A 242 GLN A 249 1 8 HELIX 13 AB4 MET A 250 ILE A 255 5 6 HELIX 14 AB5 GLY A 260 GLY A 271 1 12 HELIX 15 AB6 TYR A 274 PHE A 281 5 8 HELIX 16 AB7 THR A 282 GLY A 291 1 10 HELIX 17 AB8 GLY A 291 CYS A 302 1 12 HELIX 18 AB9 PRO A 326 ALA A 330 5 5 HELIX 19 AC1 THR A 333 ASP A 360 1 28 HELIX 20 AC2 ASP A 391 LYS A 404 1 14 HELIX 21 AC3 ASN A 405 ASN A 407 5 3 SHEET 1 AA1 6 ILE A 109 SER A 113 0 SHEET 2 AA1 6 GLU A 116 ASP A 120 -1 O GLU A 116 N ALA A 112 SHEET 3 AA1 6 VAL A 9 MET A 14 -1 N VAL A 12 O ALA A 117 SHEET 4 AA1 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9 SHEET 5 AA1 6 GLN A 235 LEU A 237 1 O THR A 236 N ILE A 216 SHEET 6 AA1 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237 SHEET 1 AA2 3 GLY A 46 VAL A 50 0 SHEET 2 AA2 3 CYS A 34 ALA A 38 -1 N VAL A 36 O ILE A 48 SHEET 3 AA2 3 LEU A 76 GLN A 79 1 O ALA A 78 N ALA A 35 SHEET 1 AA3 2 GLU A 82 SER A 83 0 SHEET 2 AA3 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83 SHEET 1 AA4 4 ILE A 319 ASN A 324 0 SHEET 2 AA4 4 LEU A 419 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA4 4 ARG A 361 VAL A 372 -1 N VAL A 367 O CYS A 425 SHEET 4 AA4 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368 LINK O3' DT T 3 P 8OG T 4 1555 1555 1.60 LINK O3' 8OG T 4 P DA T 5 1555 1555 1.60 LINK OD1 ASP A 13 CA CA A 502 1555 1555 2.61 LINK OD2 ASP A 13 CA CA A 502 1555 1555 2.54 LINK OD1 ASP A 13 CA CA A 503 1555 1555 2.43 LINK O MET A 14 CA CA A 502 1555 1555 2.33 LINK OD2 ASP A 115 CA CA A 502 1555 1555 2.28 LINK OD1 ASP A 115 CA CA A 503 1555 1555 2.36 LINK OE2 GLU A 116 CA CA A 503 1555 1555 2.27 LINK O1A DCP A 501 CA CA A 502 1555 1555 2.39 LINK O1B DCP A 501 CA CA A 502 1555 1555 2.34 LINK O1G DCP A 501 CA CA A 502 1555 1555 2.28 LINK O1A DCP A 501 CA CA A 503 1555 1555 2.36 LINK CA CA A 503 O HOH A 875 1555 1555 2.32 LINK CA CA A 503 O3' DT P 8 1555 1555 2.45 CISPEP 1 LEU A 150 PRO A 151 0 3.69 CISPEP 2 LYS A 231 PRO A 232 0 -4.80 CISPEP 3 GLN A 412 THR A 413 0 0.61 CISPEP 4 SER A 416 PRO A 417 0 -7.45 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 ASP A 115 LYS A 231 SITE 4 AC1 27 CA A 502 CA A 503 HOH A 819 HOH A 825 SITE 5 AC1 27 HOH A 826 HOH A 830 HOH A 831 HOH A 854 SITE 6 AC1 27 HOH A 862 HOH A 864 HOH A 867 HOH A 875 SITE 7 AC1 27 DT P 8 HOH P 118 8OG T 4 SITE 1 AC2 5 ASP A 13 MET A 14 ASP A 115 DCP A 501 SITE 2 AC2 5 CA A 503 SITE 1 AC3 7 ASP A 13 ASP A 115 GLU A 116 DCP A 501 SITE 2 AC3 7 CA A 502 HOH A 875 DT P 8 SITE 1 AC4 10 ARG A 24 PRO A 244 PHE A 247 SER A 248 SITE 2 AC4 10 GLY A 276 GLU A 277 HOH A 638 HOH A 658 SITE 3 AC4 10 HOH A 665 HOH A 785 SITE 1 AC5 8 ARG A 111 ALA A 112 SER A 113 ILE A 114 SITE 2 AC5 8 HOH A 864 DT P 8 HOH P 118 DG T 7 CRYST1 98.769 98.769 81.966 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 0.010125 0.005845 0.000000 0.00000 SCALE2 0.000000 0.011691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012200 0.00000