PDB Short entry for 4DL2 HEADER TRANSFERASE/DNA/INHIBITOR 05-FEB-12 4DL2 TITLE HUMAN DNA POLYMERASE ETA INSERTING DCMPNPP OPPOSITE CG TEMPLATE (GG0A) 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: DNA (5'-D(*AP*CP*GP*GP*CP*TP*CP*AP*CP*AP*CP*T)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*TP*AP*GP*TP*GP*TP*GP*AP*G)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: DCMPNPP 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: OLIGONUCLEOTIDE, CHAIN T; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: OLIGONUCLEOTIDE, CHAIN P KEYWDS CISPLATIN, CHEMORESISTENCE, TRANSLESION SYNTHESIS, HUMAN DNA KEYWDS 2 POLYMERSE ETA, KINETICS, MOLECULAR SPLINT, INHIBITION, DNA KEYWDS 3 DISTORSION, SECOND TLS POLYMERASE, NUCLEOTIDYL TRANSFER REACTION, KEYWDS 4 PCNA, TRANSFERASE-DNA-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHAO,C.BIERTUMPFEL,M.GREGORY,Y.HUA,F.HANAOKA,W.YANG REVDAT 3 13-SEP-23 4DL2 1 REMARK SEQADV LINK REVDAT 2 26-JUN-13 4DL2 1 JRNL REVDAT 1 09-MAY-12 4DL2 0 JRNL AUTH Y.ZHAO,C.BIERTUMPFEL,M.T.GREGORY,Y.J.HUA,F.HANAOKA,W.YANG JRNL TITL STRUCTURAL BASIS FOR CHEMORESISTANCE TO CISPLATIN MEDIATED JRNL TITL 2 BY DNA POLYMERASE ETA JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 7269 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22529383 JRNL DOI 10.1073/PNAS.1202681109 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 23814 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.690 REMARK 3 FREE R VALUE TEST SET COUNT : 1832 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 20.0000 - 5.0284 0.98 1695 148 0.2053 0.2233 REMARK 3 2 5.0284 - 4.0026 1.00 1718 127 0.1632 0.1806 REMARK 3 3 4.0026 - 3.5000 1.00 1689 149 0.1699 0.1943 REMARK 3 4 3.5000 - 3.1815 1.00 1708 137 0.1708 0.2143 REMARK 3 5 3.1815 - 2.9543 1.00 1702 131 0.1861 0.1852 REMARK 3 6 2.9543 - 2.7807 1.00 1697 134 0.2021 0.2136 REMARK 3 7 2.7807 - 2.6418 1.00 1678 144 0.2136 0.2459 REMARK 3 8 2.6418 - 2.5270 1.00 1697 134 0.2099 0.2521 REMARK 3 9 2.5270 - 2.4299 1.00 1669 160 0.2291 0.2578 REMARK 3 10 2.4299 - 2.3462 1.00 1638 169 0.2169 0.2721 REMARK 3 11 2.3462 - 2.2730 1.00 1702 123 0.2229 0.2809 REMARK 3 12 2.2730 - 2.2081 1.00 1707 131 0.2286 0.2633 REMARK 3 13 2.2081 - 2.1500 1.00 1682 145 0.2336 0.2852 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.61 REMARK 3 K_SOL : 0.44 REMARK 3 B_SOL : 48.14 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.610 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.41270 REMARK 3 B22 (A**2) : 1.41270 REMARK 3 B33 (A**2) : 3.75150 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 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 : 0.004 4028 REMARK 3 ANGLE : 0.849 5557 REMARK 3 CHIRALITY : 0.049 623 REMARK 3 PLANARITY : 0.006 629 REMARK 3 DIHEDRAL : 19.851 1589 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 4DL2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070463. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE SI(220) CRYSTAL AND REMARK 200 MIRROR VERTICAL FOCUSING REMARK 200 OPTICS : DOUBLE SI(220) CRYSTAL AND REMARK 200 MIRROR VERTICAL FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23818 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : 0.09000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : 0.56500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3MR2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, MGCL2, PEG 2K-MME, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 26.84333 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 53.68667 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 40.26500 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 67.10833 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 13.42167 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: 5000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 -2 REMARK 465 PRO A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 155 REMARK 465 THR A 156 REMARK 465 ALA A 157 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 GLU A 158 CG CD OE1 OE2 REMARK 470 GLU A 159 CG CD OE1 OE2 REMARK 470 DA T 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA T 1 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA T 1 C2 N3 C4 REMARK 470 DT P 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT P 1 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT P 1 C7 C6 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 DG T 3 O3' DG T 3 C3' -0.074 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 3 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG T 3 O4' - C1' - N9 ANGL. DEV. = 3.3 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 58.35 33.66 REMARK 500 TYR A 39 70.66 62.28 REMARK 500 SER A 62 31.19 70.13 REMARK 500 SER A 257 -4.65 86.44 REMARK 500 GLN A 412 -11.07 78.92 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 OD1 REMARK 620 2 MET A 14 O 85.5 REMARK 620 3 ASP A 115 OD1 93.4 81.3 REMARK 620 4 0KX P 10 O1A 99.0 171.3 91.0 REMARK 620 5 0KX P 10 O2B 172.7 98.7 93.1 77.6 REMARK 620 6 0KX P 10 O2G 83.1 108.5 169.3 79.5 89.9 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 OD2 REMARK 620 2 ASP A 115 OD2 93.1 REMARK 620 3 GLU A 116 OE2 86.3 93.6 REMARK 620 4 HOH A 787 O 84.8 174.3 91.5 REMARK 620 5 DG P 9 O3' 163.0 83.5 77.3 100.0 REMARK 620 6 DG P 9 O3' 161.2 81.2 76.2 102.5 2.7 REMARK 620 7 0KX P 10 O1A 99.4 91.6 172.0 83.6 97.4 98.6 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 P 10 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 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MR2 RELATED DB: PDB REMARK 900 RELATED ID: 3MR3 RELATED DB: PDB REMARK 900 RELATED ID: 3MR5 RELATED DB: PDB REMARK 900 RELATED ID: 3MR6 RELATED DB: PDB REMARK 900 RELATED ID: 3SI8 RELATED DB: PDB REMARK 900 RELATED ID: 4DL3 RELATED DB: PDB REMARK 900 RELATED ID: 4DL4 RELATED DB: PDB REMARK 900 RELATED ID: 4DL5 RELATED DB: PDB REMARK 900 RELATED ID: 4DL6 RELATED DB: PDB REMARK 900 RELATED ID: 4DL7 RELATED DB: PDB DBREF 4DL2 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 4DL2 T 1 12 PDB 4DL2 4DL2 1 12 DBREF 4DL2 P 1 9 PDB 4DL2 4DL2 1 9 SEQADV 4DL2 GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 4DL2 PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 4DL2 HIS A 0 UNP Q9Y253 EXPRESSION TAG 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 GLN 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 ARG 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 DA DC DG DG DC DT DC DA DC DA DC DT SEQRES 1 P 9 DT DA DG DT DG DT DG DA DG HET MG A 502 1 HET MG A 503 1 HET GOL A 504 6 HET GOL A 505 6 HET GOL A 506 6 HET 0KX P 10 28 HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 MG 2(MG 2+) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 9 0KX C9 H17 N4 O12 P3 FORMUL 10 HOH *218(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 ALA A 65 CYS A 72 1 8 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 GLU A 158 VAL A 161 5 4 HELIX 9 9 GLN A 162 LEU A 178 1 17 HELIX 10 10 SER A 185 GLY A 209 1 25 HELIX 11 11 ASN A 219 ASN A 230 1 12 HELIX 12 12 SER A 242 GLN A 249 1 8 HELIX 13 13 MET A 250 ILE A 255 5 6 HELIX 14 14 GLY A 260 GLY A 271 1 12 HELIX 15 15 TYR A 274 PHE A 281 5 8 HELIX 16 16 THR A 282 GLY A 291 1 10 HELIX 17 17 GLY A 291 CYS A 302 1 12 HELIX 18 18 PRO A 326 ALA A 330 5 5 HELIX 19 19 ARG A 334 ASP A 360 1 27 HELIX 20 20 ASP A 391 LYS A 404 1 14 HELIX 21 21 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 ALA A 10 O VAL A 119 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 ALA A 214 SHEET 6 A 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237 SHEET 1 B 4 MET A 63 TRP A 64 0 SHEET 2 B 4 GLY A 46 VAL A 50 -1 N ILE A 47 O MET A 63 SHEET 3 B 4 CYS A 34 GLN A 38 -1 N VAL A 36 O ILE A 48 SHEET 4 B 4 LEU A 76 GLN A 79 1 O ALA A 78 N ALA A 35 SHEET 1 C 2 ARG A 81 SER A 83 0 SHEET 2 C 2 LYS A 86 ASN A 88 -1 O ASN A 88 N ARG A 81 SHEET 1 D 3 ILE A 319 ASN A 324 0 SHEET 2 D 3 GLU A 414 ALA A 431 -1 O LEU A 424 N CYS A 321 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 LEU A 424 N CYS A 321 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 OD1 ASP A 13 MG MG A 502 1555 1555 2.02 LINK OD2 ASP A 13 MG MG A 503 1555 1555 2.12 LINK O MET A 14 MG MG A 502 1555 1555 2.13 LINK OD1 ASP A 115 MG MG A 502 1555 1555 2.25 LINK OD2 ASP A 115 MG MG A 503 1555 1555 2.36 LINK OE2 GLU A 116 MG MG A 503 1555 1555 2.40 LINK MG MG A 502 O1A 0KX P 10 1555 1555 2.15 LINK MG MG A 502 O2B 0KX P 10 1555 1555 2.19 LINK MG MG A 502 O2G 0KX P 10 1555 1555 2.27 LINK MG MG A 503 O HOH A 787 1555 1555 2.35 LINK MG MG A 503 O3'B DG P 9 1555 1555 2.40 LINK MG MG A 503 O3'A DG P 9 1555 1555 2.52 LINK MG MG A 503 O1A 0KX P 10 1555 1555 2.26 CISPEP 1 LEU A 150 PRO A 151 0 1.73 CISPEP 2 LYS A 231 PRO A 232 0 -0.16 CISPEP 3 SER A 416 PRO A 417 0 0.32 SITE 1 AC1 23 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC1 23 PHE A 17 PHE A 18 ILE A 48 ALA A 49 SITE 3 AC1 23 TYR A 52 ARG A 55 ARG A 61 ASP A 115 SITE 4 AC1 23 LYS A 231 MG A 502 MG A 503 HOH A 630 SITE 5 AC1 23 HOH A 643 HOH A 648 HOH A 787 HOH A 788 SITE 6 AC1 23 HOH A 789 DG P 9 DG T 4 SITE 1 AC2 5 ASP A 13 MET A 14 ASP A 115 MG A 503 SITE 2 AC2 5 0KX P 10 SITE 1 AC3 7 ASP A 13 ASP A 115 GLU A 116 MG A 502 SITE 2 AC3 7 HOH A 787 DG P 9 0KX P 10 SITE 1 AC4 11 ARG A 24 GLN A 25 PRO A 244 PHE A 247 SITE 2 AC4 11 SER A 248 GLY A 276 GLU A 277 HOH A 604 SITE 3 AC4 11 HOH A 620 HOH A 689 HOH A 757 SITE 1 AC5 7 GLN A 20 GLN A 23 ARG A 24 ARG A 30 SITE 2 AC5 7 GLY A 209 PHE A 210 HOH A 738 SITE 1 AC6 8 ASN A 26 PRO A 27 HIS A 28 GLY A 271 SITE 2 AC6 8 ILE A 272 GLU A 273 TYR A 274 GLU A 277 CRYST1 97.860 97.860 80.530 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 0.010219 0.005900 0.000000 0.00000 SCALE2 0.000000 0.011800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012418 0.00000