HEADER TRANSFERASE/DNA 29-JUL-16 5L1I TITLE CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING DCTP OPPOSITE TITLE 2 O6-METHYL-2'-DEOXYGUANOSINE 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*(6OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*C)-3'); COMPND 13 CHAIN: P; COMPND 14 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 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS CATALYTIC DOMAIN, DNA DAMAGE, DNA POLYMERASE, LESION BYPASS, O6- KEYWDS 2 METHYL-2'-DEOXYGUANOSINE, Y-FAMILY POLYMERASE, TRANSLESION DNA KEYWDS 3 SYNTHESIS (TLS), DNA BINDING PROTEIN., TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PATRA,M.EGLI REVDAT 6 04-OCT-23 5L1I 1 REMARK REVDAT 5 23-MAR-22 5L1I 1 LINK REVDAT 4 20-SEP-17 5L1I 1 JRNL REVDAT 3 23-NOV-16 5L1I 1 JRNL REVDAT 2 19-OCT-16 5L1I 1 JRNL REVDAT 1 05-OCT-16 5L1I 0 JRNL AUTH A.PATRA,Q.ZHANG,F.P.GUENGERICH,M.EGLI JRNL TITL MECHANISMS OF INSERTION OF DCTP AND DTTP OPPOSITE THE DNA JRNL TITL 2 LESION O6-METHYL-2'-DEOXYGUANOSINE BY HUMAN DNA POLYMERASE JRNL TITL 3 ETA. JRNL REF J.BIOL.CHEM. V. 291 24304 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27694439 JRNL DOI 10.1074/JBC.M116.755462 REMARK 2 REMARK 2 RESOLUTION. 2.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0151 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 10962 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 594 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) : 2.78 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.86 REMARK 3 REFLECTION IN BIN (WORKING SET) : 825 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3366 REMARK 3 NUCLEIC ACID ATOMS : 409 REMARK 3 HETEROGEN ATOMS : 42 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) : 49.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.39000 REMARK 3 B12 (A**2) : -0.06000 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): 0.389 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.304 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.955 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3927 ; 0.010 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3602 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5385 ; 1.523 ; 1.880 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8300 ; 1.038 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 428 ; 6.775 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;39.649 ;23.987 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 633 ;16.267 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;19.129 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 584 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4108 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 880 ; 0.001 ; 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): 1718 ; 2.948 ; 4.767 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1717 ; 2.948 ; 4.766 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2144 ; 4.847 ; 7.134 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2145 ; 4.846 ; 7.136 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2209 ; 3.096 ; 5.155 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2209 ; 3.093 ; 5.155 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3242 ; 5.000 ; 7.647 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4489 ; 8.010 ;54.532 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4468 ; 7.994 ;54.524 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 : NULL 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 5L1I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000222972. 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 : 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-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 : 11577 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.780 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.16900 REMARK 200 R SYM (I) : 0.16900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6470 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.96600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.579 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: 4O3N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5.5, 5MM CALCIUM REMARK 280 CHLORIDE, 15% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 27.28967 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 54.57933 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 40.93450 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 68.22417 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 13.64483 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: 6780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 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: 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 58.89 31.26 REMARK 500 TYR A 39 86.95 66.35 REMARK 500 SER A 62 -50.31 82.48 REMARK 500 MET A 63 130.88 -32.29 REMARK 500 CYS A 72 83.40 -153.35 REMARK 500 GLN A 179 53.61 -99.07 REMARK 500 SER A 217 -151.64 -153.40 REMARK 500 SER A 257 -4.40 87.92 REMARK 500 ARG A 313 93.20 -160.21 REMARK 500 ARG A 382 118.72 -161.37 REMARK 500 LYS A 404 -52.40 -142.42 REMARK 500 ASN A 405 -60.37 -6.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 724 DISTANCE = 5.96 ANGSTROMS 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 50.9 REMARK 620 3 MET A 14 O 73.5 101.6 REMARK 620 4 ASP A 115 OD2 104.9 70.0 78.5 REMARK 620 5 DCP A 501 O2A 115.6 79.4 167.0 89.9 REMARK 620 6 DCP A 501 O2B 151.6 157.4 89.6 93.5 85.4 REMARK 620 7 DCP A 501 O2G 79.9 112.3 105.3 174.7 86.0 82.9 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 OD2 REMARK 620 2 ASP A 115 OD1 85.4 REMARK 620 3 GLU A 116 OE2 94.2 121.5 REMARK 620 4 DCP A 501 O2A 79.5 83.4 154.0 REMARK 620 5 HOH A 650 O 88.2 157.2 80.7 73.9 REMARK 620 6 DT P 8 O3' 152.8 101.6 103.9 75.4 75.1 REMARK 620 7 DC P 9 OP2 146.0 61.0 99.0 100.1 124.6 50.9 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 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5L1L RELATED DB: PDB REMARK 900 RELATED ID: 5L1K RELATED DB: PDB REMARK 900 RELATED ID: 5L1J RELATED DB: PDB DBREF 5L1I A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 5L1I T 1 12 PDB 5L1I 5L1I 1 12 DBREF 5L1I P 1 9 PDB 5L1I 5L1I 1 9 SEQADV 5L1I GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 5L1I PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 5L1I 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 DC DA DT 6OG DA DT DG DA DC DG DC DT SEQRES 1 P 9 DA DG DC DG DT DC DA DT DC HET 6OG 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 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 6OG C11 H16 N5 O7 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 *138(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 41 GLY A 45 5 5 HELIX 4 AA4 SER A 51 ALA A 56 1 6 HELIX 5 AA5 TRP A 64 CYS A 72 1 9 HELIX 6 AA6 LEU A 89 ARG A 105 1 17 HELIX 7 AA7 LEU A 121 LEU A 132 1 12 HELIX 8 AA8 SER A 138 LEU A 142 5 5 HELIX 9 AA9 GLN A 162 SER A 177 1 16 HELIX 10 AB1 SER A 185 GLY A 209 1 25 HELIX 11 AB2 ASN A 219 ASN A 230 1 12 HELIX 12 AB3 SER A 239 GLY A 241 5 3 HELIX 13 AB4 SER A 242 GLN A 249 1 8 HELIX 14 AB5 PRO A 251 ILE A 255 5 5 HELIX 15 AB6 GLY A 260 GLY A 271 1 12 HELIX 16 AB7 TYR A 274 PHE A 281 5 8 HELIX 17 AB8 THR A 282 GLY A 291 1 10 HELIX 18 AB9 GLY A 291 CYS A 302 1 12 HELIX 19 AC1 PRO A 326 ALA A 330 5 5 HELIX 20 AC2 ARG A 334 ASP A 360 1 27 HELIX 21 AC3 ASP A 391 VAL A 402 1 12 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 ALA A 10 O VAL A 119 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 ALA A 214 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 ALA A 35 SHEET 1 AA3 4 ILE A 319 ASN A 324 0 SHEET 2 AA3 4 MET A 421 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA3 4 ARG A 361 ARG A 371 -1 N GLN A 365 O THR A 427 SHEET 4 AA3 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368 SHEET 1 AA4 2 LEU A 331 THR A 333 0 SHEET 2 AA4 2 GLU A 414 LEU A 419 -1 O LEU A 419 N LEU A 331 LINK O3' DT T 3 P 6OG T 4 1555 1555 1.62 LINK O3' 6OG T 4 P DA T 5 1555 1555 1.59 LINK OD1 ASP A 13 CA CA A 502 1555 1555 2.58 LINK OD2 ASP A 13 CA CA A 502 1555 1555 2.52 LINK OD2 ASP A 13 CA CA A 503 1555 1555 2.31 LINK O MET A 14 CA CA A 502 1555 1555 2.29 LINK OD2 ASP A 115 CA CA A 502 1555 1555 2.31 LINK OD1 ASP A 115 CA CA A 503 1555 1555 2.54 LINK OE2 GLU A 116 CA CA A 503 1555 1555 2.35 LINK O2A DCP A 501 CA CA A 502 1555 1555 2.23 LINK O2B DCP A 501 CA CA A 502 1555 1555 2.18 LINK O2G DCP A 501 CA CA A 502 1555 1555 2.21 LINK O2A DCP A 501 CA CA A 503 1555 1555 2.45 LINK CA CA A 503 O HOH A 650 1555 1555 2.38 LINK CA CA A 503 O3' DT P 8 1555 1555 3.16 LINK CA CA A 503 OP2 DC P 9 1555 1555 2.23 CISPEP 1 LEU A 150 PRO A 151 0 5.49 CISPEP 2 LYS A 231 PRO A 232 0 -8.59 CISPEP 3 SER A 416 PRO A 417 0 -11.26 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 CA A 502 CA A 503 HOH A 609 SITE 5 AC1 21 HOH A 650 HOH A 658 DT P 8 DC P 9 SITE 6 AC1 21 6OG 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 8 ASP A 13 ASP A 115 GLU A 116 DCP A 501 SITE 2 AC3 8 CA A 502 HOH A 650 DT P 8 DC P 9 SITE 1 AC4 8 ARG A 24 PRO A 244 PHE A 247 SER A 248 SITE 2 AC4 8 GLY A 276 GLU A 277 HOH A 623 HOH A 631 SITE 1 AC5 4 SER A 257 LYS A 293 ASN A 294 TRP A 297 CRYST1 99.095 99.095 81.869 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 0.010091 0.005826 0.000000 0.00000 SCALE2 0.000000 0.011652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012215 0.00000