HEADER TRANSFERASE, LYASE/DNA 11-AUG-14 4UB5 TITLE DNA POLYMERASE BETA SUBSTRATE COMPLEX WITH A TEMPLATING CYTOSINE, TITLE 2 INCOMING 8-OXODGTP, AND MN2+, 5 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*C)-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 4UB5 1 REMARK LINK REVDAT 4 27-NOV-19 4UB5 1 SOURCE JRNL REMARK REVDAT 3 04-FEB-15 4UB5 1 JRNL REVDAT 2 03-DEC-14 4UB5 1 JRNL REVDAT 1 12-NOV-14 4UB5 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. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 3 NUMBER OF REFLECTIONS : 39111 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.700 REMARK 3 FREE R VALUE TEST SET COUNT : 3403 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 21.0880 - 6.1477 0.98 1670 170 0.1985 0.2241 REMARK 3 2 6.1477 - 4.8997 0.97 1684 162 0.1900 0.2831 REMARK 3 3 4.8997 - 4.2863 0.94 1629 160 0.1578 0.1933 REMARK 3 4 4.2863 - 3.8971 0.95 1645 160 0.1637 0.2126 REMARK 3 5 3.8971 - 3.6192 0.97 1681 156 0.1824 0.2704 REMARK 3 6 3.6192 - 3.4068 0.99 1715 168 0.2081 0.2904 REMARK 3 7 3.4068 - 3.2368 0.99 1683 153 0.2377 0.2891 REMARK 3 8 3.2368 - 3.0964 0.96 1677 155 0.2371 0.2970 REMARK 3 9 3.0964 - 2.9775 0.88 1519 144 0.2594 0.3248 REMARK 3 10 2.9775 - 2.8750 0.84 1459 140 0.2507 0.3464 REMARK 3 11 2.8750 - 2.7853 0.82 1426 130 0.2708 0.3783 REMARK 3 12 2.7853 - 2.7059 0.82 1414 127 0.3103 0.4510 REMARK 3 13 2.7059 - 2.6348 0.80 1375 134 0.3170 0.3641 REMARK 3 14 2.6348 - 2.5706 0.80 1370 136 0.3096 0.3861 REMARK 3 15 2.5706 - 2.5123 0.82 1411 128 0.2973 0.3885 REMARK 3 16 2.5123 - 2.4589 0.78 1360 125 0.3042 0.3566 REMARK 3 17 2.4589 - 2.4098 0.79 1380 133 0.2921 0.3574 REMARK 3 18 2.4098 - 2.3644 0.82 1411 138 0.2829 0.3155 REMARK 3 19 2.3644 - 2.3222 0.82 1399 144 0.2908 0.3527 REMARK 3 20 2.3222 - 2.2829 0.76 1290 115 0.3214 0.4350 REMARK 3 21 2.2829 - 2.2461 0.84 1521 143 0.2947 0.3962 REMARK 3 22 2.2461 - 2.2116 0.85 1407 135 0.2963 0.3495 REMARK 3 23 2.2116 - 2.1791 0.77 1378 133 0.3295 0.3452 REMARK 3 24 2.1791 - 2.1500 0.70 1204 114 0.3434 0.4107 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 : 0.37 REMARK 3 B_SOL : 39.50 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.500 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) : -2.58880 REMARK 3 B22 (A**2) : 3.08130 REMARK 3 B33 (A**2) : -0.49250 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.54340 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 3334 REMARK 3 ANGLE : 0.926 4662 REMARK 3 CHIRALITY : 0.057 505 REMARK 3 PLANARITY : 0.003 481 REMARK 3 DIHEDRAL : 20.344 1290 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 4UB5 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_1000203118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-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 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39111 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 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 : 3.200 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.51600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 45.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 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 38.85650 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: 6260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 PRO A 208 REMARK 465 LYS A 244 REMARK 465 ASN A 245 REMARK 465 ASP A 246 REMARK 465 GLU A 247 REMARK 465 LYS A 248 REMARK 465 LEU A 301 REMARK 465 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 GLY A 305 REMARK 465 VAL A 306 REMARK 465 ALA A 307 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 71 CG CD OE1 OE2 REMARK 470 GLN A 90 CG CD OE1 NE2 REMARK 470 PRO A 300 CG CD REMARK 470 GLN A 324 CG CD OE1 NE2 REMARK 470 TRP A 325 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 325 CZ3 CH2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 LYS A 331 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 160 N CA C O CB CG OD1 REMARK 480 ASP A 160 OD2 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 DG T 3 O4' - C1' - N9 ANGL. DEV. = 1.8 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 170 130.94 -172.11 REMARK 500 CYS A 178 -143.99 -113.89 REMARK 500 ASP A 190 -167.15 -164.27 REMARK 500 GLU A 295 1.39 -67.23 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 MN T 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG T 3 N7 REMARK 620 2 HOH T 202 O 74.5 REMARK 620 3 HOH T 215 O 85.9 158.9 REMARK 620 4 HOH D 101 O 104.1 91.8 100.6 REMARK 620 5 HOH A 515 O 168.1 111.0 86.9 86.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 HOH P 204 O 90.9 REMARK 620 3 THR A 101 O 163.6 81.5 REMARK 620 4 VAL A 103 O 94.5 174.5 93.2 REMARK 620 5 ILE A 106 O 103.6 93.2 91.3 85.7 REMARK 620 6 HOH A 576 O 83.3 95.7 83.0 84.8 168.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 10 O3' REMARK 620 2 ASP A 190 OD2 160.7 REMARK 620 3 ASP A 192 OD1 91.7 105.2 REMARK 620 4 ASP A 256 OD2 73.6 96.1 92.5 REMARK 620 5 8DG A 403 O1A 95.5 94.2 88.1 169.1 REMARK 620 6 HOH A 574 O 89.7 73.6 177.9 89.3 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN P 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH P 208 O REMARK 620 2 8DG A 403 O2A 82.5 REMARK 620 3 HOH A 541 O 84.3 110.3 REMARK 620 4 HOH A 571 O 161.0 102.2 110.6 REMARK 620 5 HOH A 572 O 86.6 88.6 157.6 75.3 REMARK 620 6 HOH A 573 O 90.6 172.9 67.3 84.9 92.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC D 3 OP1 REMARK 620 2 HOH D 102 O 84.3 REMARK 620 3 LYS A 60 O 160.0 89.3 REMARK 620 4 LEU A 62 O 91.5 169.3 91.3 REMARK 620 5 VAL A 65 O 72.4 89.6 88.7 79.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 92.7 REMARK 620 3 8DG A 403 O1B 169.3 92.4 REMARK 620 4 8DG A 403 O3G 82.3 174.5 92.2 REMARK 620 5 8DG A 403 O1A 97.3 86.0 92.5 96.8 REMARK 620 6 HOH A 575 O 91.9 83.2 79.4 94.8 166.1 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 MN T 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN P 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN P 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8DG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405 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: 4UB3 RELATED DB: PDB REMARK 900 RELATED ID: 4UB4 RELATED DB: PDB REMARK 900 RELATED ID: 4UBB RELATED DB: PDB REMARK 900 RELATED ID: 4UBC RELATED DB: PDB DBREF 4UB5 T 1 16 PDB 4UB5 4UB5 1 16 DBREF 4UB5 P 1 10 PDB 4UB5 4UB5 1 10 DBREF 4UB5 D 1 5 PDB 4UB5 4UB5 1 5 DBREF 4UB5 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 10 DG DC DT DG DA DT DG DC DG 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 MN T 101 1 HET MN P 101 1 HET MN P 102 1 HET MN A 401 1 HET MN A 402 1 HET 8DG A 403 44 HET NA A 404 1 HET NA A 405 1 HETNAM MN MANGANESE (II) ION HETNAM 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM NA SODIUM ION FORMUL 5 MN 5(MN 2+) FORMUL 10 8DG C10 H16 N5 O14 P3 FORMUL 11 NA 2(NA 1+) FORMUL 13 HOH *109(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 LYS A 127 1 7 HELIX 9 AA9 ASN A 128 LEU A 132 5 5 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 LYS A 168 1 17 HELIX 13 AB4 CYS A 178 ARG A 183 1 6 HELIX 14 AB5 LEU A 210 VAL A 221 1 12 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 ASP A 256 N VAL A 193 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 THR A 292 ILE A 293 0 SHEET 2 AA3 2 ILE A 298 ARG A 299 -1 O ARG A 299 N THR A 292 LINK N7 DG T 3 MN MN T 101 1555 1555 2.63 LINK MN MN T 101 O HOH T 202 1555 1555 2.19 LINK MN MN T 101 O HOH T 215 1555 1555 2.17 LINK MN MN T 101 O HOH D 101 1555 1555 2.20 LINK MN MN T 101 O HOH A 515 1555 1556 2.19 LINK N7 DG P 4 MN MN P 102 1555 1555 2.56 LINK OP1 DG P 9 NA NA A 404 1555 1555 2.50 LINK O3' DC P 10 MN MN A 401 1555 1555 2.23 LINK MN MN P 101 O HOH P 208 1555 1555 2.22 LINK MN MN P 101 O2A 8DG A 403 1555 1555 2.21 LINK MN MN P 101 O HOH A 541 1555 1555 2.22 LINK MN MN P 101 O HOH A 571 1555 1555 2.19 LINK MN MN P 101 O HOH A 572 1555 1555 2.21 LINK MN MN P 101 O HOH A 573 1555 1555 2.20 LINK O HOH P 204 NA NA A 404 1555 1555 2.36 LINK OP1 DC D 3 NA NA A 405 1555 1555 2.56 LINK O HOH D 102 NA NA A 405 1555 1555 2.43 LINK O LYS A 60 NA NA A 405 1555 1555 2.43 LINK O LEU A 62 NA NA A 405 1555 1555 2.46 LINK O VAL A 65 NA NA A 405 1555 1555 2.50 LINK O THR A 101 NA NA A 404 1555 1555 2.27 LINK O VAL A 103 NA NA A 404 1555 1555 2.45 LINK O ILE A 106 NA NA A 404 1555 1555 2.52 LINK OD2 ASP A 190 MN MN A 401 1555 1555 2.11 LINK OD1 ASP A 190 MN MN A 402 1555 1555 2.10 LINK OD1 ASP A 192 MN MN A 401 1555 1555 2.11 LINK OD2 ASP A 192 MN MN A 402 1555 1555 2.15 LINK OD2 ASP A 256 MN MN A 401 1555 1555 2.17 LINK MN MN A 401 O1A 8DG A 403 1555 1555 2.14 LINK MN MN A 401 O HOH A 574 1555 1555 2.22 LINK MN MN A 402 O1B 8DG A 403 1555 1555 2.07 LINK MN MN A 402 O3G 8DG A 403 1555 1555 2.33 LINK MN MN A 402 O1A 8DG A 403 1555 1555 2.04 LINK MN MN A 402 O HOH A 575 1555 1555 2.19 LINK NA NA A 404 O HOH A 576 1555 1555 2.39 CISPEP 1 GLY A 274 SER A 275 0 2.42 SITE 1 AC1 5 HOH A 515 HOH D 101 DG T 3 HOH T 202 SITE 2 AC1 5 HOH T 215 SITE 1 AC2 6 8DG A 403 HOH A 541 HOH A 571 HOH A 572 SITE 2 AC2 6 HOH A 573 HOH P 208 SITE 1 AC3 1 DG P 4 SITE 1 AC4 7 ASP A 190 ASP A 192 ASP A 256 MN A 402 SITE 2 AC4 7 8DG A 403 HOH A 574 DC P 10 SITE 1 AC5 5 ASP A 190 ASP A 192 MN A 401 8DG A 403 SITE 2 AC5 5 HOH A 575 SITE 1 AC6 28 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC6 28 SER A 188 GLY A 189 ASP A 190 ASP A 192 SITE 3 AC6 28 TYR A 271 PHE A 272 THR A 273 GLY A 274 SITE 4 AC6 28 ASP A 276 ASN A 279 ARG A 283 MN A 401 SITE 5 AC6 28 MN A 402 HOH A 527 HOH A 541 HOH A 571 SITE 6 AC6 28 HOH A 572 HOH A 574 HOH A 575 DC P 10 SITE 7 AC6 28 MN P 101 HOH P 208 DC T 6 DG T 7 SITE 1 AC7 6 THR A 101 VAL A 103 ILE A 106 HOH A 576 SITE 2 AC7 6 DG P 9 HOH P 204 SITE 1 AC8 5 LYS A 60 LEU A 62 VAL A 65 DC D 3 SITE 2 AC8 5 HOH D 102 CRYST1 55.066 77.713 55.112 90.00 114.24 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 0.018160 0.000000 0.008177 0.00000 SCALE2 0.000000 0.012868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019899 0.00000