HEADER TRANSFERASE, LYASE/DNA 11-AUG-14 4UB3 TITLE DNA POLYMERASE BETA CLOSED PRODUCT COMPLEX WITH A TEMPLATING CYTOSINE TITLE 2 AND 8-OXODGMP, 60 S COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'; COMPND 3 CHAIN: T; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(8OG))-3'; COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(P*GP*TP*CP*GP*G)-3'; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA POLYMERASE BETA; COMPND 15 CHAIN: A; COMPND 16 EC: 2.7.7.7,4.2.99.-; COMPND 17 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; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: TAP56; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PWL11 KEYWDS DNA POLYMERASE, TRANSFERASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,S.H.WILSON,W.A.BEARD REVDAT 5 27-SEP-23 4UB3 1 REMARK LINK REVDAT 4 27-NOV-19 4UB3 1 SOURCE JRNL REMARK REVDAT 3 04-FEB-15 4UB3 1 JRNL REVDAT 2 03-DEC-14 4UB3 1 JRNL REVDAT 1 12-NOV-14 4UB3 0 JRNL AUTH B.D.FREUDENTHAL,W.A.BEARD,L.PERERA,D.D.SHOCK,T.KIM, JRNL AUTH 2 T.SCHLICK,S.H.WILSON JRNL TITL UNCOVERING THE POLYMERASE-INDUCED CYTOTOXICITY OF AN JRNL TITL 2 OXIDIZED NUCLEOTIDE. JRNL REF NATURE V. 517 635 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 25409153 JRNL DOI 10.1038/NATURE13886 REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.1 REMARK 3 NUMBER OF REFLECTIONS : 21786 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1086 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 21.3441 - 4.1049 0.96 3048 160 0.1605 0.2019 REMARK 3 2 4.1049 - 3.2619 0.96 3020 152 0.1968 0.2357 REMARK 3 3 3.2619 - 2.8507 0.82 2576 133 0.2303 0.3067 REMARK 3 4 2.8507 - 2.5905 0.73 2254 116 0.2549 0.3379 REMARK 3 5 2.5905 - 2.4051 0.73 2255 121 0.2939 0.3811 REMARK 3 6 2.4051 - 2.2635 0.81 2512 141 0.2537 0.3675 REMARK 3 7 2.2635 - 2.1502 0.85 2650 140 0.2639 0.3555 REMARK 3 8 2.1502 - 2.0600 0.77 2385 123 0.3000 0.3485 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 : 0.34 REMARK 3 B_SOL : 29.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.600 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) : 4.87030 REMARK 3 B22 (A**2) : -1.69000 REMARK 3 B33 (A**2) : -3.19170 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 4.21220 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 : 0.014 3514 REMARK 3 ANGLE : 1.073 4906 REMARK 3 CHIRALITY : 0.056 527 REMARK 3 PLANARITY : 0.003 513 REMARK 3 DIHEDRAL : 20.481 1397 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 4UB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000203116. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 HF 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 : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27186 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 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 (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.51100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: PDB ENTRY 2FMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 350 MM SODIUM REMARK 280 CHLORIDE, 17% PEG3350, PH 8.0, 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 40.04700 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: 5740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 465 THR A 10 REMARK 465 GLY A 302 REMARK 465 VAL A 303 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 248 CG CD CE NZ REMARK 470 GLU A 309 CG CD OE1 OE2 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 DC P 10 C5' DC P 10 C4' 0.053 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. = 2.6 DEGREES REMARK 500 DC T 8 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC T 16 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG P 1 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA P 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC P 8 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG P 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC D 3 O4' - C1' - N1 ANGL. DEV. = 2.3 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 ASP A 170 118.88 -168.48 REMARK 500 CYS A 178 -139.69 -116.48 REMARK 500 ASP A 190 -165.17 -167.45 REMARK 500 LYS A 230 116.66 -162.33 REMARK 500 ASP A 246 -12.63 71.98 REMARK 500 SER A 275 -177.24 -68.24 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 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 10 O3' REMARK 620 2 8OG P 11 OP2 63.3 REMARK 620 3 ASP A 190 OD1 124.6 61.8 REMARK 620 4 ASP A 190 OD2 144.2 97.8 43.0 REMARK 620 5 ASP A 192 OD1 106.0 84.5 75.7 101.7 REMARK 620 6 ASP A 256 OD2 86.4 149.7 148.0 108.0 104.9 REMARK 620 N 1 2 3 4 5 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 8OG P 11 OP1 REMARK 620 2 HOH P 203 O 93.6 REMARK 620 3 HOH P 207 O 108.4 94.1 REMARK 620 4 HOH P 215 O 76.8 82.6 174.1 REMARK 620 5 PPV A 402 O12 85.8 165.5 99.9 83.1 REMARK 620 6 PPV A 402 O12 92.9 167.7 93.8 88.7 8.2 REMARK 620 7 HOH A 612 O 169.3 82.7 81.9 92.8 95.3 89.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 8OG P 11 OP2 REMARK 620 2 ASP A 190 OD1 87.6 REMARK 620 3 ASP A 192 OD2 77.1 94.7 REMARK 620 4 PPV A 402 O12 64.0 129.9 115.7 REMARK 620 5 PPV A 402 O12 73.7 142.4 111.8 13.2 REMARK 620 6 PPV A 402 O32 101.9 170.5 86.6 56.9 43.9 REMARK 620 7 PPV A 402 O32 112.6 159.9 89.1 64.4 51.2 10.7 REMARK 620 8 PPV A 402 O11 118.6 97.1 160.7 67.1 66.1 79.4 74.7 REMARK 620 9 PPV A 402 O21 115.9 87.3 166.9 71.9 73.0 89.5 84.8 10.1 REMARK 620 N 1 2 3 4 5 6 7 8 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 MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UAW RELATED DB: PDB REMARK 900 RELATED ID: 4UAY RELATED DB: PDB REMARK 900 RELATED ID: 4UAZ RELATED DB: PDB REMARK 900 RELATED ID: 4UB1 RELATED DB: PDB REMARK 900 RELATED ID: 4UB2 RELATED DB: PDB REMARK 900 RELATED ID: 4UB4 RELATED DB: PDB REMARK 900 RELATED ID: 4UB5 RELATED DB: PDB REMARK 900 RELATED ID: 4UBB RELATED DB: PDB REMARK 900 RELATED ID: 4UBC RELATED DB: PDB DBREF 4UB3 T 1 16 PDB 4UB3 4UB3 1 16 DBREF 4UB3 P 1 11 PDB 4UB3 4UB3 1 11 DBREF 4UB3 D 1 5 PDB 4UB3 4UB3 1 5 DBREF 4UB3 A 1 335 UNP P06746 DPOLB_HUMAN 1 335 SEQRES 1 T 16 DC DC DG DA DC DC DG 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 DC 8OG 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 11 23 HET MG P 101 1 HET MG A 401 1 HET PPV A 402 18 HET NA A 403 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM PPV PYROPHOSPHATE HETNAM NA SODIUM ION 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 7 PPV H4 O7 P2 FORMUL 8 NA NA 1+ FORMUL 9 HOH *173(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 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 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 GLY A 144 LYS A 148 5 5 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 GLY A 290 1 16 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 GLY A 237 O ILE A 255 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N SER A 229 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' DC P 10 P 8OG P 11 1555 1555 1.61 LINK O3' DC P 10 NA NA A 403 1555 1555 2.57 LINK OP1 8OG P 11 MG MG P 101 1555 1555 2.01 LINK OP2 8OG P 11 MG MG A 401 1555 1555 2.16 LINK OP2 8OG P 11 NA NA A 403 1555 1555 2.23 LINK MG MG P 101 O HOH P 203 1555 1555 1.97 LINK MG MG P 101 O HOH P 207 1555 1555 2.01 LINK MG MG P 101 O HOH P 215 1555 1555 2.13 LINK MG MG P 101 O12APPV A 402 1555 1555 1.98 LINK MG MG P 101 O12BPPV A 402 1555 1555 2.57 LINK MG MG P 101 O HOH A 612 1555 1555 2.03 LINK OD1 ASP A 190 MG MG A 401 1555 1555 2.04 LINK OD1 ASP A 190 NA NA A 403 1555 1555 3.19 LINK OD2 ASP A 190 NA NA A 403 1555 1555 2.11 LINK OD2 ASP A 192 MG MG A 401 1555 1555 2.21 LINK OD1 ASP A 192 NA NA A 403 1555 1555 2.26 LINK OD2 ASP A 256 NA NA A 403 1555 1555 2.16 LINK MG MG A 401 O12APPV A 402 1555 1555 2.93 LINK MG MG A 401 O12BPPV A 402 1555 1555 2.92 LINK MG MG A 401 O32APPV A 402 1555 1555 1.94 LINK MG MG A 401 O32BPPV A 402 1555 1555 2.68 LINK MG MG A 401 O11BPPV A 402 1555 1555 2.94 LINK MG MG A 401 O21APPV A 402 1555 1555 2.32 LINK MG MG A 401 O HOH A 544 1555 1555 2.15 CISPEP 1 GLY A 274 SER A 275 0 5.66 SITE 1 AC1 6 PPV A 402 HOH A 612 8OG P 11 HOH P 203 SITE 2 AC1 6 HOH P 207 HOH P 215 SITE 1 AC2 5 ASP A 190 ASP A 192 PPV A 402 HOH A 544 SITE 2 AC2 5 8OG P 11 SITE 1 AC3 16 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC3 16 SER A 188 GLY A 189 ASP A 190 ASP A 192 SITE 3 AC3 16 MG A 401 HOH A 538 HOH A 544 HOH A 612 SITE 4 AC3 16 8OG P 11 MG P 101 HOH P 207 HOH P 215 SITE 1 AC4 5 ASP A 190 ASP A 192 ASP A 256 DC P 10 SITE 2 AC4 5 8OG P 11 CRYST1 50.698 80.094 55.358 90.00 107.80 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 0.019725 0.000000 0.006333 0.00000 SCALE2 0.000000 0.012485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018972 0.00000