PDB Short entry for 5V1J HEADER TRANSFERASE/DNA, LIGASE/DNA 02-MAR-17 5V1J TITLE DNA POLYMERASE BETA OPEN PRODUCT COMPLEX WITH 8-OXOG:C AND INSERTED TITLE 2 DCTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7,4.2.99.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 8 3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG)P*C)-3'); COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 17 CHAIN: D; COMPND 18 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: POLB; 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; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630 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 06-MAR-24 5V1J 1 LINK REVDAT 4 01-JAN-20 5V1J 1 REMARK REVDAT 3 03-JAN-18 5V1J 1 REMARK REVDAT 2 13-SEP-17 5V1J 1 JRNL REVDAT 1 10-MAY-17 5V1J 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. 2.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_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) : 2.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 25305 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2532 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 31.7636 - 6.8344 0.96 1288 147 0.1698 0.1954 REMARK 3 2 6.8344 - 5.4335 0.98 1334 143 0.1978 0.2487 REMARK 3 3 5.4335 - 4.7492 0.97 1317 146 0.1800 0.2323 REMARK 3 4 4.7492 - 4.3161 0.95 1291 140 0.1920 0.2637 REMARK 3 5 4.3161 - 4.0074 0.95 1256 149 0.1804 0.2292 REMARK 3 6 4.0074 - 3.7716 0.96 1311 138 0.1982 0.2873 REMARK 3 7 3.7716 - 3.5829 0.97 1339 136 0.2103 0.2544 REMARK 3 8 3.5829 - 3.4272 0.96 1298 153 0.2060 0.2667 REMARK 3 9 3.4272 - 3.2954 0.96 1290 145 0.2174 0.3077 REMARK 3 10 3.2954 - 3.1818 0.95 1281 143 0.2255 0.3142 REMARK 3 11 3.1818 - 3.0824 0.94 1251 142 0.3024 0.4670 REMARK 3 12 3.0824 - 2.9943 0.91 1263 145 0.3744 0.4259 REMARK 3 13 2.9943 - 2.9155 0.89 1179 123 0.3436 0.4993 REMARK 3 14 2.9155 - 2.8445 0.91 1249 146 0.3216 0.4321 REMARK 3 15 2.8445 - 2.7798 0.90 1193 134 0.3016 0.3784 REMARK 3 16 2.7798 - 2.7207 0.92 1292 137 0.3080 0.3903 REMARK 3 17 2.7207 - 2.6663 0.92 1195 151 0.3075 0.4767 REMARK 3 18 2.6663 - 2.6160 0.85 1146 114 0.3487 0.4063 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.730 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 : 0.009 3211 REMARK 3 ANGLE : 1.134 4488 REMARK 3 CHIRALITY : 0.058 504 REMARK 3 PLANARITY : 0.007 474 REMARK 3 DIHEDRAL : 20.839 1796 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 5V1J 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_1000226219. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : 25305 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.616 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 350 MM SODIUM REMARK 280 ACETATE, 17% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 39.89750 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: 4900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D 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 465 THR A 10 REMARK 465 LEU A 11 REMARK 465 ASN A 12 REMARK 465 LYS A 244 REMARK 465 ASN A 245 REMARK 465 ASP A 246 REMARK 465 GLU A 247 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 ARG A 40 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 LEU A 82 CG CD1 CD2 REMARK 470 ARG A 83 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 85 CG CD1 CD2 REMARK 470 GLU A 86 CG CD OE1 OE2 REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 GLN A 90 CG CD OE1 NE2 REMARK 470 LYS A 113 CG CD CE NZ REMARK 470 LYS A 127 CG CD CE NZ REMARK 470 ARG A 149 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 150 CD1 REMARK 470 ARG A 152 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 153 CG CD OE1 OE2 REMARK 470 GLN A 157 CG CD OE1 NE2 REMARK 470 VAL A 166 CG1 CG2 REMARK 470 LYS A 167 CG CD CE NZ REMARK 470 SER A 171 OG REMARK 470 ARG A 183 CG CD NE CZ NH1 NH2 REMARK 470 SER A 199 OG REMARK 470 SER A 202 OG REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 THR A 205 OG1 CG2 REMARK 470 LYS A 206 CG 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 GLN A 240 CG CD OE1 NE2 REMARK 470 LEU A 259 CG CD1 CD2 REMARK 470 LYS A 262 CG CD CE NZ REMARK 470 ILE A 277 CG1 CG2 CD1 REMARK 470 LYS A 280 CG CD CE NZ REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 LYS A 289 CG CD CE NZ REMARK 470 ARG A 299 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 303 CG1 CG2 REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 GLU A 329 CG CD OE1 OE2 REMARK 470 LYS A 331 CG CD CE NZ REMARK 470 GLU A 335 CG CD OE1 OE2 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 NH1 ARG A 182 OE2 GLU A 316 2.05 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 8 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG T 15 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC T 16 O4' - C1' - N1 ANGL. DEV. = 2.0 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 PRO A 50 36.06 -93.82 REMARK 500 GLN A 90 -167.36 -73.61 REMARK 500 ASP A 91 78.01 64.44 REMARK 500 ASP A 170 104.06 -175.69 REMARK 500 CYS A 178 -163.90 -116.38 REMARK 500 ALA A 185 150.29 -49.73 REMARK 500 SER A 204 -158.51 -161.28 REMARK 500 THR A 205 -90.20 -140.39 REMARK 500 LYS A 206 -14.79 80.00 REMARK 500 SER A 229 145.31 178.37 REMARK 500 GLN A 240 142.86 -171.52 REMARK 500 ARG A 333 48.81 -89.69 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 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 91.6 REMARK 620 3 VAL A 65 O 69.6 78.5 REMARK 620 4 DC D 3 OP1 152.5 88.4 83.5 REMARK 620 5 HOH D 102 O 81.0 139.1 61.2 81.0 REMARK 620 N 1 2 3 4 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 THR A 101 O REMARK 620 2 VAL A 103 O 88.5 REMARK 620 3 ILE A 106 O 79.3 73.6 REMARK 620 4 HOH A 517 O 101.3 103.1 176.6 REMARK 620 5 DG P 9 OP1 162.5 88.8 83.3 96.2 REMARK 620 6 HOH P 101 O 79.9 144.0 70.9 112.5 92.3 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 NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 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: 5VII 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 5V1J A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 5V1J T 1 16 PDB 5V1J 5V1J 1 16 DBREF 5V1J P 1 11 PDB 5V1J 5V1J 1 11 DBREF 5V1J D 1 5 PDB 5V1J 5V1J 1 5 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 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 HET 8OG P 10 23 HET NA A 401 1 HET NA A 402 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM NA SODIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 3 8OG C10 H14 N5 O8 P FORMUL 5 NA 2(NA 1+) FORMUL 7 HOH *32(H2 O) HELIX 1 AA1 GLY A 13 VAL A 29 1 17 HELIX 2 AA2 ALA A 32 TYR A 49 1 18 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 GLN A 90 1 9 HELIX 6 AA6 ASP A 91 ARG A 102 1 12 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 GLU A 147 1 6 HELIX 12 AB3 ARG A 152 ASP A 170 1 19 HELIX 13 AB4 LEU A 211 VAL A 221 1 11 HELIX 14 AB5 PRO A 261 GLY A 274 1 14 HELIX 15 AB6 SER A 275 LYS A 289 1 15 HELIX 16 AB7 SER A 315 ILE A 323 1 9 HELIX 17 AB8 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 CYS A 178 0 SHEET 2 AA2 5 MET A 191 THR A 196 -1 O ASP A 192 N CYS A 178 SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ASP A 256 N MET A 191 SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N GLY A 237 O ILE A 255 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 1.61 LINK O LYS A 60 NA NA A 402 1555 1555 2.72 LINK O LEU A 62 NA NA A 402 1555 1555 2.45 LINK O VAL A 65 NA NA A 402 1555 1555 3.10 LINK O THR A 101 NA NA A 401 1555 1555 2.29 LINK O VAL A 103 NA NA A 401 1555 1555 2.91 LINK O ILE A 106 NA NA A 401 1555 1555 2.74 LINK NA NA A 401 O HOH A 517 1555 1555 2.61 LINK NA NA A 401 OP1 DG P 9 1555 1555 2.38 LINK NA NA A 401 O HOH P 101 1555 1555 2.96 LINK NA NA A 402 OP1 DC D 3 1555 1555 3.07 LINK NA NA A 402 O HOH D 102 1555 1555 2.28 CISPEP 1 GLY A 274 SER A 275 0 3.34 SITE 1 AC1 6 THR A 101 VAL A 103 ILE A 106 HOH A 517 SITE 2 AC1 6 DG P 9 HOH P 101 SITE 1 AC2 5 LYS A 60 LEU A 62 VAL A 65 DC D 3 SITE 2 AC2 5 HOH D 102 CRYST1 55.273 79.795 55.887 90.00 110.29 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 0.018092 0.000000 0.006690 0.00000 SCALE2 0.000000 0.012532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019077 0.00000