HEADER TRANSFERASE/DNA 29-MAR-21 7M87 TITLE HUMAN DNA POL ETA S113A WITH DA-ENDED PRIMER AND DATP: IN CRYSTALLO TITLE 2 REACTION FOR 230 S 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(*CP*AP*TP*TP*TP*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*AP*A)-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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS DNA POLYMERASE, TIME RESOLVED CRYSTALLOGRAPHY, DEPROTONATION, DNA KEYWDS 2 BINDING PROTEIN, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.T.GREGORY,Y.GAO,W.YANG REVDAT 3 18-OCT-23 7M87 1 REMARK REVDAT 2 14-JUL-21 7M87 1 JRNL REVDAT 1 02-JUN-21 7M87 0 JRNL AUTH M.T.GREGORY,Y.GAO,Q.CUI,W.YANG JRNL TITL MULTIPLE DEPROTONATION PATHS OF THE NUCLEOPHILE 3'-OH IN THE JRNL TITL 2 DNA SYNTHESIS REACTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 34088846 JRNL DOI 10.1073/PNAS.2103990118 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 38238 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.670 REMARK 3 FREE R VALUE TEST SET COUNT : 2933 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 29.9400 - 5.1000 1.00 1727 147 0.1871 0.2089 REMARK 3 2 5.0900 - 4.0500 1.00 1731 127 0.1611 0.1605 REMARK 3 3 4.0500 - 3.5400 1.00 1671 148 0.1608 0.1766 REMARK 3 4 3.5400 - 3.2100 1.00 1699 139 0.1773 0.1989 REMARK 3 5 3.2100 - 2.9800 1.00 1693 129 0.2003 0.2314 REMARK 3 6 2.9800 - 2.8100 1.00 1689 136 0.2133 0.2261 REMARK 3 7 2.8100 - 2.6700 1.00 1679 144 0.2141 0.2285 REMARK 3 8 2.6700 - 2.5500 1.00 1696 134 0.2189 0.2455 REMARK 3 9 2.5500 - 2.4500 1.00 1659 162 0.2290 0.2364 REMARK 3 10 2.4500 - 2.3700 1.00 1664 167 0.2085 0.2539 REMARK 3 11 2.3700 - 2.2900 1.00 1693 128 0.2082 0.2773 REMARK 3 12 2.2900 - 2.2300 0.99 1684 126 0.2134 0.2570 REMARK 3 13 2.2300 - 2.1700 1.00 1669 146 0.2115 0.2548 REMARK 3 14 2.1700 - 2.1200 1.00 1702 147 0.2125 0.2781 REMARK 3 15 2.1200 - 2.0700 1.00 1680 117 0.2147 0.2770 REMARK 3 16 2.0700 - 2.0300 0.99 1670 145 0.2274 0.2389 REMARK 3 17 2.0300 - 1.9800 0.99 1677 141 0.2361 0.2854 REMARK 3 18 1.9800 - 1.9500 1.00 1655 139 0.2380 0.2572 REMARK 3 19 1.9500 - 1.9100 0.99 1673 129 0.2646 0.3523 REMARK 3 20 1.9100 - 1.8800 0.99 1683 128 0.2878 0.3444 REMARK 3 21 1.8800 - 1.8500 0.98 1611 154 0.3080 0.3364 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) : 23.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.63 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 4217 REMARK 3 ANGLE : 1.062 5853 REMARK 3 CHIRALITY : 0.060 657 REMARK 3 PLANARITY : 0.007 667 REMARK 3 DIHEDRAL : 27.900 1690 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 7M87 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255857. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 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 REMARK 200 MONOCHROMATOR : NULL 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 : 38284 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.80500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4ECQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 2000 MME, 100 MM MES, PH 6, REMARK 280 EVAPORATION, TEMPERATURE 295K 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 27.31167 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 54.62333 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 40.96750 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 68.27917 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 13.65583 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: 6530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 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 465 THR A 160 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 127 CD OE1 OE2 REMARK 470 GLN A 130 CD OE1 NE2 REMARK 470 LYS A 131 CD CE NZ REMARK 470 GLN A 133 CG CD OE1 NE2 REMARK 470 GLN A 135 CG CD OE1 NE2 REMARK 470 GLN A 169 CG CD OE1 NE2 REMARK 470 GLN A 179 CG CD OE1 NE2 REMARK 470 LYS A 328 CG CD CE NZ REMARK 470 ARG A 371 NE CZ NH1 NH2 REMARK 470 LYS A 376 CG CD CE NZ REMARK 470 LEU A 378 CG CD1 CD2 REMARK 470 GLN A 412 CG CD OE1 NE2 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: 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 63.19 27.58 REMARK 500 TYR A 39 160.19 73.01 REMARK 500 SER A 62 -12.34 82.14 REMARK 500 SER A 217 -159.68 -154.73 REMARK 500 ASN A 230 49.72 -141.04 REMARK 500 SER A 257 -10.63 96.18 REMARK 500 SER A 409 130.91 -39.81 REMARK 500 MET A 421 138.59 -172.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 176 -11.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH T 103 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 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 ASP A 13 OD1 23.5 REMARK 620 3 ASP A 115 OD1 99.0 85.1 REMARK 620 4 GLU A 116 OE2 93.1 116.1 112.6 REMARK 620 5 DTP A 504 O2A 95.5 77.2 92.6 151.7 REMARK 620 6 HOH A 678 O 82.3 89.1 160.5 86.6 67.9 REMARK 620 7 DA P 8 O3' 162.5 146.4 91.0 96.3 69.6 83.5 REMARK 620 8 DA P 8 O3' 163.5 146.6 64.9 90.1 89.2 114.0 31.5 REMARK 620 9 DA P 8 O3' 159.6 142.9 90.9 99.5 66.1 82.5 3.5 33.4 REMARK 620 N 1 2 3 4 5 6 7 8 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 45.8 REMARK 620 3 MET A 14 O 109.2 78.9 REMARK 620 4 ASP A 115 OD2 81.0 111.3 84.0 REMARK 620 5 DTP A 504 O1B 158.5 154.7 87.9 88.4 REMARK 620 6 DTP A 504 O2A 77.2 109.1 171.9 92.4 84.8 REMARK 620 7 DTP A 504 O3G 109.4 78.4 94.1 169.4 81.1 88.2 REMARK 620 N 1 2 3 4 5 6 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 MET A 14 O 88.5 REMARK 620 3 ASP A 115 OD2 81.7 84.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG P 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DPO A 505 O3 REMARK 620 2 HOH A 703 O 96.8 REMARK 620 3 HOH A 774 O 172.6 84.4 REMARK 620 4 HOH A 818 O 103.4 87.4 69.2 REMARK 620 5 HOH A 885 O 94.9 92.7 92.4 161.6 REMARK 620 6 DA P 9 OP2 89.3 171.5 88.8 85.4 92.7 REMARK 620 N 1 2 3 4 5 DBREF 7M87 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 7M87 T 1 12 PDB 7M87 7M87 1 12 DBREF 7M87 P 1 9 PDB 7M87 7M87 1 9 SEQADV 7M87 GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 7M87 PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 7M87 HIS A 0 UNP Q9Y253 EXPRESSION TAG SEQADV 7M87 ALA A 113 UNP Q9Y253 SER 113 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 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 ALA 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 DT DT DT DG DA DC DG DC DT SEQRES 1 P 9 DA DG DC DG DT DC DA DA DA HET MG A 501 1 HET CA A 502 1 HET MG A 503 1 HET DTP A 504 30 HET DPO A 505 9 HET GOL A 506 6 HET GOL A 507 6 HET GOL A 508 6 HET MG P 101 1 HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM DPO DIPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 MG 3(MG 2+) FORMUL 5 CA CA 2+ FORMUL 7 DTP C10 H16 N5 O12 P3 FORMUL 8 DPO O7 P2 4- FORMUL 9 GOL 3(C3 H8 O3) FORMUL 13 HOH *496(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 GLN A 133 1 13 HELIX 7 AA7 SER A 138 LEU A 142 5 5 HELIX 8 AA8 GLN A 162 SER A 177 1 16 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 ARG A 334 ASP A 360 1 27 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 ALA A 113 0 SHEET 2 AA1 6 GLU A 116 ASP A 120 -1 O TYR A 118 N GLU A 110 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 GLN 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 VAL A 37 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 3 ILE A 319 ASN A 324 0 SHEET 2 AA4 3 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA4 3 LEU A 331 THR A 333 -1 N ALA A 332 O TRP A 415 SHEET 1 AA5 4 ILE A 319 ASN A 324 0 SHEET 2 AA5 4 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA5 4 ARG A 361 VAL A 372 -1 N VAL A 367 O CYS A 425 SHEET 4 AA5 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368 LINK OD1AASP A 13 MG MG A 501 1555 1555 2.05 LINK OD1BASP A 13 MG MG A 501 1555 1555 2.92 LINK OD1AASP A 13 CA A CA A 502 1555 1555 3.05 LINK OD2AASP A 13 CA A CA A 502 1555 1555 2.27 LINK OD1BASP A 13 MG B MG A 503 1555 1555 2.15 LINK O MET A 14 CA A CA A 502 1555 1555 2.29 LINK O MET A 14 MG B MG A 503 1555 1555 2.26 LINK OD1 ASP A 115 MG MG A 501 1555 1555 2.31 LINK OD2 ASP A 115 CA A CA A 502 1555 1555 2.23 LINK OD2 ASP A 115 MG B MG A 503 1555 1555 2.24 LINK OE2 GLU A 116 MG MG A 501 1555 1555 2.18 LINK MG MG A 501 O2AADTP A 504 1555 1555 2.51 LINK MG MG A 501 O HOH A 678 1555 1555 2.57 LINK MG MG A 501 O3'A DA P 8 1555 1555 2.21 LINK MG MG A 501 O3'B DA P 8 1555 1555 3.00 LINK MG MG A 501 O3'C DA P 8 1555 1555 2.28 LINK MG MG A 501 OP1C DA P 9 1555 1555 2.19 LINK CA A CA A 502 O1BADTP A 504 1555 1555 2.30 LINK CA A CA A 502 O2AADTP A 504 1555 1555 2.30 LINK CA A CA A 502 O3GADTP A 504 1555 1555 2.33 LINK O3 CDPO A 505 MG C MG P 101 1555 1555 2.02 LINK O HOH A 703 MG C MG P 101 1555 1555 2.75 LINK O HOH A 774 MG C MG P 101 1555 1555 2.09 LINK O HOH A 818 MG C MG P 101 1555 1555 2.88 LINK O CHOH A 885 MG C MG P 101 1555 1555 2.09 LINK OP2C DA P 9 MG C MG P 101 1555 1555 2.19 CISPEP 1 LEU A 150 PRO A 151 0 2.51 CISPEP 2 LYS A 231 PRO A 232 0 0.07 CISPEP 3 SER A 416 PRO A 417 0 -4.87 CRYST1 98.262 98.262 81.935 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 0.010177 0.005876 0.000000 0.00000 SCALE2 0.000000 0.011751 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012205 0.00000