PDB Short entry for 5V1I HEADER TRANSFERASE/DNA, LIGASE/DNA 02-MAR-17 5V1I TITLE DNA POLYMERASE BETA TERNARY PRODUCT COMPLEX WITH 8-OXOG:C AND INSERTED TITLE 2 DCTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 3 3'); COMPND 4 CHAIN: T; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG)P*C)-3'); COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA POLYMERASE BETA; COMPND 16 CHAIN: A; COMPND 17 EC: 2.7.7.7,4.2.99.-; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: POLB; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE LIGASE / DNA, TRANSFERASE-DNA, LIGASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,M.R.SMITH,A.M.WHITAKER,M.A.SCHAICH REVDAT 5 04-OCT-23 5V1I 1 LINK REVDAT 4 01-JAN-20 5V1I 1 REMARK REVDAT 3 04-APR-18 5V1I 1 REMARK REVDAT 2 13-SEP-17 5V1I 1 JRNL REVDAT 1 10-MAY-17 5V1I 0 JRNL AUTH A.M.WHITAKER,M.R.SMITH,M.A.SCHAICH,B.D.FREUDENTHAL JRNL TITL CAPTURING A MAMMALIAN DNA POLYMERASE EXTENDING FROM AN JRNL TITL 2 OXIDIZED NUCLEOTIDE. JRNL REF NUCLEIC ACIDS RES. V. 45 6934 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28449123 JRNL DOI 10.1093/NAR/GKX293 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.1 REMARK 3 NUMBER OF REFLECTIONS : 47232 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.580 REMARK 3 FREE R VALUE TEST SET COUNT : 3579 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 24.5974 - 6.0019 0.96 1810 153 0.1556 0.2164 REMARK 3 2 6.0019 - 4.7753 0.97 1825 150 0.1651 0.1966 REMARK 3 3 4.7753 - 4.1750 0.97 1812 149 0.1357 0.1603 REMARK 3 4 4.1750 - 3.7948 0.98 1854 155 0.1372 0.1691 REMARK 3 5 3.7948 - 3.5236 0.97 1847 153 0.1485 0.2012 REMARK 3 6 3.5236 - 3.3164 0.97 1835 151 0.1578 0.2017 REMARK 3 7 3.3164 - 3.1506 0.97 1796 156 0.1770 0.2438 REMARK 3 8 3.1506 - 3.0137 0.96 1836 153 0.2147 0.2660 REMARK 3 9 3.0137 - 2.8979 0.95 1793 150 0.2258 0.2731 REMARK 3 10 2.8979 - 2.7981 0.95 1794 142 0.2159 0.2920 REMARK 3 11 2.7981 - 2.7107 0.96 1784 148 0.2196 0.3023 REMARK 3 12 2.7107 - 2.6333 0.95 1789 148 0.2097 0.3133 REMARK 3 13 2.6333 - 2.5640 0.96 1801 150 0.2130 0.2627 REMARK 3 14 2.5640 - 2.5015 0.96 1798 153 0.2126 0.3183 REMARK 3 15 2.5015 - 2.4447 0.96 1836 145 0.2136 0.2867 REMARK 3 16 2.4447 - 2.3927 0.95 1777 143 0.2206 0.2686 REMARK 3 17 2.3927 - 2.3449 0.93 1745 141 0.2120 0.3573 REMARK 3 18 2.3449 - 2.3007 0.87 1607 126 0.2291 0.2604 REMARK 3 19 2.3007 - 2.2596 0.87 1658 134 0.2246 0.2609 REMARK 3 20 2.2596 - 2.2214 0.83 1560 133 0.2333 0.2662 REMARK 3 21 2.2214 - 2.1856 0.82 1582 123 0.2322 0.2969 REMARK 3 22 2.1856 - 2.1520 0.80 1480 120 0.2295 0.2754 REMARK 3 23 2.1520 - 2.1203 0.75 1408 113 0.2300 0.2466 REMARK 3 24 2.1203 - 2.0905 0.73 1348 112 0.2300 0.3092 REMARK 3 25 2.0905 - 2.0622 0.69 1337 105 0.2464 0.2863 REMARK 3 26 2.0622 - 2.0355 0.50 941 73 0.2707 0.3902 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.460 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 3381 REMARK 3 ANGLE : 0.892 4716 REMARK 3 CHIRALITY : 0.048 520 REMARK 3 PLANARITY : 0.005 502 REMARK 3 DIHEDRAL : 18.027 1924 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 5V1I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226210. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47251 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.035 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2FMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 350 MM SODIUM REMARK 280 CHLORIDE, 17% PEG3350, PH 8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.89900 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -136.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, D, A 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 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 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 LYS A 52 CG CD CE NZ REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 GLN A 90 CG CD OE1 NE2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 LYS A 127 CG CD CE NZ REMARK 470 GLU A 129 CG CD OE1 OE2 REMARK 470 LYS A 131 CE NZ REMARK 470 ARG A 137 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 153 CG CD OE1 OE2 REMARK 470 LYS A 206 CD CE NZ REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 GLU A 216 CG CD OE1 OE2 REMARK 470 LYS A 220 CE NZ REMARK 470 LYS A 244 CE NZ REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 280 CD CE NZ REMARK 470 VAL A 303 CG1 CG2 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 T 101 O HOH T 132 2.12 REMARK 500 O HOH A 594 O HOH A 682 2.18 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 DC T 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC P 11 O4' - C1' - N1 ANGL. DEV. = 2.2 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 ASP A 170 117.99 -160.04 REMARK 500 CYS A 178 -138.08 -114.19 REMARK 500 ASP A 246 -1.27 66.98 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 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 HOH P 201 O 90.1 REMARK 620 3 THR A 101 O 165.4 78.4 REMARK 620 4 VAL A 103 O 97.3 172.4 94.6 REMARK 620 5 ILE A 106 O 93.3 88.3 95.2 89.5 REMARK 620 6 HOH A 674 O 89.6 90.4 81.6 91.4 176.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 409 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 8OG P 10 O3' REMARK 620 2 DC P 11 OP1 59.8 REMARK 620 3 ASP A 190 OD2 124.8 90.0 REMARK 620 4 ASP A 192 OD1 108.4 87.2 115.4 REMARK 620 5 ASP A 256 OD2 92.3 152.0 106.3 105.1 REMARK 620 N 1 2 3 4 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 DC P 11 OP2 REMARK 620 2 HOH P 205 O 84.1 REMARK 620 3 PPV A 408 O32 79.6 152.2 REMARK 620 4 PPV A 408 O32 83.9 160.9 8.9 REMARK 620 5 HOH A 568 O 83.9 97.0 103.6 96.4 REMARK 620 6 HOH A 577 O 87.3 80.8 76.0 83.9 171.1 REMARK 620 7 HOH A 628 O 168.3 100.1 92.1 89.1 106.2 82.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 407 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 11 OP1 REMARK 620 2 ASP A 190 OD1 91.9 REMARK 620 3 ASP A 192 OD2 95.8 96.7 REMARK 620 4 PPV A 408 O12 98.2 162.7 96.2 REMARK 620 5 PPV A 408 O12 104.0 157.0 98.2 6.4 REMARK 620 6 PPV A 408 O11 93.9 84.1 170.2 81.3 78.4 REMARK 620 7 HOH A 517 O 100.6 75.5 162.0 88.8 85.1 10.8 REMARK 620 8 HOH A 564 O 171.0 79.1 85.5 90.5 84.6 85.1 77.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC D 3 OP1 REMARK 620 2 HOH D 103 O 77.2 REMARK 620 3 LYS A 60 O 171.2 94.5 REMARK 620 4 LEU A 62 O 95.5 164.1 93.2 REMARK 620 5 VAL A 65 O 91.8 100.4 86.9 93.9 REMARK 620 6 HOH A 676 O 87.1 77.8 94.0 87.8 178.1 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 MG P 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VIF RELATED DB: PDB REMARK 900 RELATED ID: 5VIG RELATED DB: PDB REMARK 900 RELATED ID: 5VIH RELATED DB: PDB REMARK 900 RELATED ID: 5VIJ RELATED DB: PDB REMARK 900 RELATED ID: 5VIN RELATED DB: PDB REMARK 900 RELATED ID: 5VIO RELATED DB: PDB REMARK 900 RELATED ID: 5VIP RELATED DB: PDB REMARK 900 RELATED ID: 5VIR RELATED DB: PDB DBREF 5V1I T 1 16 PDB 5V1I 5V1I 1 16 DBREF 5V1I P 1 11 PDB 5V1I 5V1I 1 11 DBREF 5V1I D 1 5 PDB 5V1I 5V1I 1 5 DBREF 5V1I A 1 335 UNP P06746 DPOLB_HUMAN 1 335 SEQRES 1 T 16 DC DC DG DA DC DG DC DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 11 DG DC DT DG DA DT DG DC DG 8OG DC SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU HET 8OG P 10 23 HET MG P 101 1 HET NA A 401 1 HET NA A 402 1 HET CL A 403 1 HET CL A 404 1 HET CL A 405 1 HET CL A 406 1 HET MG A 407 1 HET PPV A 408 18 HET NA A 409 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PPV PYROPHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 5 MG 2(MG 2+) FORMUL 6 NA 3(NA 1+) FORMUL 8 CL 4(CL 1-) FORMUL 13 PPV H4 O7 P2 FORMUL 15 HOH *235(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 LYS A 48 1 17 HELIX 3 AA3 SER A 55 LYS A 61 1 7 HELIX 4 AA4 GLY A 66 GLY A 80 1 15 HELIX 5 AA5 LEU A 82 ASP A 91 1 10 HELIX 6 AA6 ASP A 91 THR A 101 1 11 HELIX 7 AA7 GLY A 107 GLU A 117 1 11 HELIX 8 AA8 THR A 121 ASN A 128 1 8 HELIX 9 AA9 GLU A 129 LEU A 132 5 4 HELIX 10 AB1 ASN A 133 TYR A 142 1 10 HELIX 11 AB2 TYR A 142 LYS A 148 1 7 HELIX 12 AB3 ARG A 152 ASP A 170 1 19 HELIX 13 AB4 CYS A 178 ARG A 183 1 6 HELIX 14 AB5 LYS A 209 VAL A 221 1 13 HELIX 15 AB6 PRO A 261 ASP A 263 5 3 HELIX 16 AB7 GLN A 264 GLY A 274 1 11 HELIX 17 AB8 SER A 275 LYS A 289 1 15 HELIX 18 AB9 SER A 315 ILE A 323 1 9 HELIX 19 AC1 GLU A 329 ARG A 333 5 5 SHEET 1 AA1 2 ILE A 150 PRO A 151 0 SHEET 2 AA1 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 AA2 5 ILE A 174 VAL A 177 0 SHEET 2 AA2 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236 SHEET 1 AA3 2 PHE A 291 ILE A 293 0 SHEET 2 AA3 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DG P 9 P 8OG P 10 1555 1555 1.60 LINK O3' 8OG P 10 P DC P 11 1555 1555 1.63 LINK OP1 DG P 9 NA NA A 401 1555 1555 2.23 LINK O3' 8OG P 10 NA NA A 409 1555 1555 2.44 LINK OP2 DC P 11 MG MG P 101 1555 1555 2.13 LINK OP1 DC P 11 MG MG A 407 1555 1555 1.97 LINK OP1 DC P 11 NA NA A 409 1555 1555 2.57 LINK MG MG P 101 O HOH P 205 1555 1555 2.03 LINK MG MG P 101 O32APPV A 408 1555 1555 2.30 LINK MG MG P 101 O32BPPV A 408 1555 1555 2.26 LINK MG MG P 101 O HOH A 568 1555 1555 2.14 LINK MG MG P 101 O HOH A 577 1555 1555 2.11 LINK MG MG P 101 O HOH A 628 1555 1555 2.08 LINK O HOH P 201 NA NA A 401 1555 1555 2.44 LINK OP1 DC D 3 NA NA A 402 1555 1555 2.57 LINK O HOH D 103 NA NA A 402 1555 1555 2.69 LINK O LYS A 60 NA NA A 402 1555 1555 2.44 LINK O LEU A 62 NA NA A 402 1555 1555 2.39 LINK O VAL A 65 NA NA A 402 1555 1555 2.36 LINK O THR A 101 NA NA A 401 1555 1555 2.33 LINK O VAL A 103 NA NA A 401 1555 1555 2.46 LINK O ILE A 106 NA NA A 401 1555 1555 2.34 LINK OD1 ASP A 190 MG MG A 407 1555 1555 2.25 LINK OD2 ASP A 190 NA NA A 409 1555 1555 2.23 LINK OD2 ASP A 192 MG MG A 407 1555 1555 2.10 LINK OD1 ASP A 192 NA NA A 409 1555 1555 2.17 LINK OD2 ASP A 256 NA NA A 409 1555 1555 2.35 LINK NA NA A 401 O HOH A 674 1555 1555 2.61 LINK NA NA A 402 O HOH A 676 1555 1555 2.40 LINK MG MG A 407 O12APPV A 408 1555 1555 2.00 LINK MG MG A 407 O12BPPV A 408 1555 1555 2.06 LINK MG MG A 407 O11APPV A 408 1555 1555 2.53 LINK MG MG A 407 O BHOH A 517 1555 1555 1.81 LINK MG MG A 407 O HOH A 564 1555 1555 2.18 CISPEP 1 GLY A 274 SER A 275 0 2.93 SITE 1 AC1 6 PPV A 408 HOH A 568 HOH A 577 HOH A 628 SITE 2 AC1 6 DC P 11 HOH P 205 SITE 1 AC2 6 THR A 101 VAL A 103 ILE A 106 HOH A 674 SITE 2 AC2 6 DG P 9 HOH P 201 SITE 1 AC3 6 LYS A 60 LEU A 62 VAL A 65 HOH A 676 SITE 2 AC3 6 DC D 3 HOH D 103 SITE 1 AC4 4 GLN A 264 TYR A 266 CYS A 267 VAL A 313 SITE 1 AC5 4 ALA A 32 ILE A 33 HIS A 34 LYS A 35 SITE 1 AC6 3 LEU A 82 GLU A 86 ARG A 89 SITE 1 AC7 3 ASN A 294 THR A 297 ARG A 299 SITE 1 AC8 7 ASP A 190 ASP A 192 PPV A 408 NA A 409 SITE 2 AC8 7 HOH A 517 HOH A 564 DC P 11 SITE 1 AC9 19 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC9 19 SER A 188 GLY A 189 ASP A 190 ASP A 192 SITE 3 AC9 19 MG A 407 HOH A 501 HOH A 517 HOH A 542 SITE 4 AC9 19 HOH A 564 HOH A 568 HOH A 577 HOH A 594 SITE 5 AC9 19 HOH A 628 DC P 11 MG P 101 SITE 1 AD1 6 ASP A 190 ASP A 192 ASP A 256 MG A 407 SITE 2 AD1 6 8OG P 10 DC P 11 CRYST1 50.564 79.798 55.539 90.00 107.62 90.00 P 1 21 1 2 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 0.019777 0.000000 0.006282 0.00000 SCALE2 0.000000 0.012532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018892 0.00000