HEADER TRANSFERASE/DNA 04-SEP-12 4GXJ TITLE R283K DNA POLYMERASE BETA TERNARY COMPLEX WITH A TEMPLATING 8OG AND TITLE 2 INCOMING DCTP ANALOG 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 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'); COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*(8OG) COMPND 17 P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 18 CHAIN: T; COMPND 19 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 EXPRESSION_SYSTEM_STRAIN: TAP56; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PWL11; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE, LYASE/DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,W.A.BEARD,S.H.WILSON REVDAT 4 13-SEP-23 4GXJ 1 REMARK SEQADV LINK REVDAT 3 17-JUL-19 4GXJ 1 REMARK LINK REVDAT 2 27-FEB-13 4GXJ 1 JRNL REVDAT 1 16-JAN-13 4GXJ 0 JRNL AUTH B.D.FREUDENTHAL,W.A.BEARD,S.H.WILSON JRNL TITL DNA POLYMERASE MINOR GROOVE INTERACTIONS MODULATE MUTAGENIC JRNL TITL 2 BYPASS OF A TEMPLATING 8-OXOGUANINE LESION. JRNL REF NUCLEIC ACIDS RES. V. 41 1848 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23267011 JRNL DOI 10.1093/NAR/GKS1276 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.5 REMARK 3 NUMBER OF REFLECTIONS : 36585 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3623 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 21.0567 - 6.4445 0.99 1455 164 0.2151 0.2450 REMARK 3 2 6.4445 - 5.1397 0.99 1434 161 0.2061 0.2628 REMARK 3 3 5.1397 - 4.4972 0.96 1425 152 0.1772 0.2289 REMARK 3 4 4.4972 - 4.0893 0.98 1428 168 0.1636 0.2213 REMARK 3 5 4.0893 - 3.7980 0.98 1463 148 0.1615 0.2369 REMARK 3 6 3.7980 - 3.5752 1.00 1490 141 0.1930 0.2644 REMARK 3 7 3.5752 - 3.3969 1.00 1461 138 0.2224 0.3019 REMARK 3 8 3.3969 - 3.2496 1.00 1441 149 0.2521 0.2900 REMARK 3 9 3.2496 - 3.1249 1.00 1510 162 0.2456 0.2847 REMARK 3 10 3.1249 - 3.0174 0.90 1321 147 0.2478 0.2998 REMARK 3 11 3.0174 - 2.9233 0.80 1171 130 0.2573 0.3732 REMARK 3 12 2.9233 - 2.8400 0.75 1100 116 0.2749 0.3447 REMARK 3 13 2.8400 - 2.7654 0.73 1046 129 0.2858 0.3330 REMARK 3 14 2.7654 - 2.6981 0.71 1025 124 0.3291 0.3787 REMARK 3 15 2.6981 - 2.6368 0.76 1113 113 0.3131 0.3792 REMARK 3 16 2.6368 - 2.5808 0.78 1188 108 0.3097 0.3558 REMARK 3 17 2.5808 - 2.5293 0.79 1122 165 0.3361 0.4282 REMARK 3 18 2.5293 - 2.4816 0.78 1146 128 0.3149 0.3964 REMARK 3 19 2.4816 - 2.4374 0.77 1120 107 0.3347 0.3557 REMARK 3 20 2.4374 - 2.3961 0.79 1173 95 0.3053 0.3987 REMARK 3 21 2.3961 - 2.3575 0.82 1256 132 0.3239 0.3560 REMARK 3 22 2.3575 - 2.3213 0.83 1158 138 0.2980 0.3938 REMARK 3 23 2.3213 - 2.2872 0.84 1223 162 0.3122 0.3884 REMARK 3 24 2.2872 - 2.2550 0.83 1223 154 0.3259 0.4120 REMARK 3 25 2.2550 - 2.2246 0.86 1233 142 0.3004 0.3865 REMARK 3 26 2.2246 - 2.1957 0.85 1237 150 0.2965 0.3568 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 : 0.41 REMARK 3 B_SOL : 44.55 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.33990 REMARK 3 B22 (A**2) : 0.38800 REMARK 3 B33 (A**2) : -0.04810 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.97780 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 3340 REMARK 3 ANGLE : 1.153 4653 REMARK 3 CHIRALITY : 0.061 505 REMARK 3 PLANARITY : 0.003 477 REMARK 3 DIHEDRAL : 21.716 1280 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 4GXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074757. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : MIRRORS VARIMAXHF REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.196 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 : 5.800 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.57900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.950 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2FMS.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM IMIDAZOLE, 350MM SODIUM ACETATE, REMARK 280 18% PEG3350, PH 8.0, VAPOR DIFFUSION, 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 38.71600 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: 6280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, P, T 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 GLU A 247 REMARK 465 LYS A 248 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 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 244 CG CD CE NZ REMARK 470 ASN A 245 CG OD1 ND2 REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 GLN A 324 CG CD OE1 NE2 REMARK 470 LYS A 326 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 TYR A 296 N CA C O CB CG CD1 REMARK 480 TYR A 296 CD2 CE1 CE2 CZ OH 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 OD2 ASP A 145 O HOH A 546 2.15 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 DT T 7 O3' - P - O5' ANGL. DEV. = -16.9 DEGREES REMARK 500 DT T 7 OP1 - P - OP2 ANGL. DEV. = 10.0 DEGREES REMARK 500 DT T 7 P - O5' - C5' ANGL. DEV. = 12.5 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 VAL A 29 -63.25 -91.72 REMARK 500 ASP A 170 124.34 -173.38 REMARK 500 CYS A 178 -153.35 -119.06 REMARK 500 HIS A 285 15.71 -68.25 REMARK 500 ASP A 314 -8.35 -145.26 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 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 94.0 REMARK 620 3 ILE A 106 O 94.3 87.6 REMARK 620 4 HOH A 504 O 79.4 86.0 170.7 REMARK 620 5 DG P 9 OP1 161.1 93.5 103.2 83.9 REMARK 620 6 HOH P 202 O 79.3 172.6 96.0 89.7 92.0 REMARK 620 N 1 2 3 4 5 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 OD2 REMARK 620 2 ASP A 192 OD1 101.3 REMARK 620 3 ASP A 256 OD2 90.7 99.3 REMARK 620 4 6CF A 401 O2A 90.7 90.5 169.6 REMARK 620 5 HOH A 502 O 79.9 173.8 86.7 83.4 REMARK 620 6 DA P 10 O3' 159.9 97.6 92.5 82.7 80.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 96.8 REMARK 620 3 6CF A 401 O1B 163.3 85.6 REMARK 620 4 6CF A 401 O2A 107.4 90.0 89.2 REMARK 620 5 6CF A 401 O2G 86.6 169.4 88.3 98.6 REMARK 620 6 HOH A 501 O 74.8 76.3 89.8 166.3 95.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 405 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 314 OD2 REMARK 620 2 HOH A 571 O 101.7 REMARK 620 3 HOH A 572 O 102.8 155.3 REMARK 620 4 HOH A 573 O 163.9 65.3 90.9 REMARK 620 N 1 2 3 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 DG P 4 N7 REMARK 620 2 HOH P 208 O 97.2 REMARK 620 N 1 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 204 O 87.4 REMARK 620 3 HOH T 214 O 90.0 85.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 6CF A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN T 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN P 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GXI RELATED DB: PDB REMARK 900 RELATED ID: 4GXK RELATED DB: PDB DBREF 4GXJ A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4GXJ T 1 16 PDB 4GXJ 4GXJ 1 16 DBREF 4GXJ P 1 10 PDB 4GXJ 4GXJ 1 10 DBREF 4GXJ D 1 5 PDB 4GXJ 4GXJ 1 5 SEQADV 4GXJ LYS A 283 UNP P06746 ARG 283 ENGINEERED MUTATION 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 LYS 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 D 5 DG DT DC DG DG SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DA SEQRES 1 T 16 DC DC DG DA DC 8OG DT DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC MODRES 4GXJ 8OG T 6 DG HET 8OG T 6 23 HET 6CF A 401 30 HET MN A 402 1 HET MN A 403 1 HET MN A 404 1 HET MN A 405 1 HET NA A 406 1 HET NA D 101 1 HET MN P 101 1 HET MN T 101 1 HET MN T 102 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 6CF 2'-DEOXY-5'-O-[(S)-{DIFLUORO[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 6CF PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]CYTIDINE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 4 8OG C10 H14 N5 O8 P FORMUL 5 6CF C10 H16 F2 N3 O12 P3 FORMUL 6 MN 7(MN 2+) FORMUL 10 NA 2(NA 1+) FORMUL 15 HOH *102(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 LYS A 48 1 17 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 ASP A 91 ARG A 102 1 12 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 ASN A 128 1 8 HELIX 9 9 GLU A 129 LEU A 132 5 4 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 LYS A 148 1 7 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 GLY A 179 ARG A 182 5 4 HELIX 14 14 LEU A 210 VAL A 221 1 12 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 GLY A 274 1 11 HELIX 17 17 SER A 275 GLU A 288 1 14 HELIX 18 18 SER A 315 GLN A 324 1 10 HELIX 19 19 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 CYS A 178 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DC T 5 P 8OG T 6 1555 1555 1.60 LINK O3' 8OG T 6 P DT T 7 1555 1555 1.57 LINK NE2 HIS A 51 MN MN A 404 1555 1555 2.11 LINK O THR A 101 NA NA A 406 1555 1555 2.20 LINK O VAL A 103 NA NA A 406 1555 1555 2.41 LINK O ILE A 106 NA NA A 406 1555 1555 2.41 LINK OD2 ASP A 190 MN MN A 402 1555 1555 2.06 LINK OD1 ASP A 190 MN MN A 403 1555 1555 2.04 LINK OD1 ASP A 192 MN MN A 402 1555 1555 2.01 LINK OD2 ASP A 192 MN MN A 403 1555 1555 2.06 LINK OD2 ASP A 256 MN MN A 402 1555 1555 2.10 LINK OD2 ASP A 314 MN MN A 405 1555 1555 2.17 LINK O2A 6CF A 401 MN MN A 402 1555 1555 2.15 LINK O1B 6CF A 401 MN MN A 403 1555 1555 2.01 LINK O2A 6CF A 401 MN MN A 403 1555 1555 2.04 LINK O2G 6CF A 401 MN MN A 403 1555 1555 2.12 LINK MN MN A 402 O HOH A 502 1555 1555 2.22 LINK MN MN A 402 O3' DA P 10 1555 1555 2.01 LINK MN MN A 403 O HOH A 501 1555 1555 2.10 LINK MN MN A 405 O HOH A 571 1555 1555 2.38 LINK MN MN A 405 O HOH A 572 1555 1555 2.15 LINK MN MN A 405 O HOH A 573 1555 1555 2.17 LINK NA NA A 406 O HOH A 504 1555 1555 2.34 LINK NA NA A 406 OP1 DG P 9 1555 1555 2.48 LINK NA NA A 406 O HOH P 202 1555 1555 2.50 LINK N7 DG P 4 MN MN P 101 1555 1555 2.28 LINK MN MN P 101 O HOH P 208 1555 1555 2.18 LINK N7 DG T 3 MN MN T 101 1555 1555 2.64 LINK MN MN T 101 O HOH T 204 1555 1555 2.13 LINK MN MN T 101 O HOH T 214 1555 1555 2.21 CISPEP 1 GLY A 274 SER A 275 0 1.53 CISPEP 2 ALA A 307 GLY A 308 0 -2.96 SITE 1 AC1 19 GLY A 179 SER A 180 ARG A 183 SER A 188 SITE 2 AC1 19 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 AC1 19 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 AC1 19 ASN A 279 MN A 402 MN A 403 HOH A 501 SITE 5 AC1 19 HOH A 502 DA P 10 8OG T 6 SITE 1 AC2 7 ASP A 190 ASP A 192 ASP A 256 6CF A 401 SITE 2 AC2 7 MN A 403 HOH A 502 DA P 10 SITE 1 AC3 5 ASP A 190 ASP A 192 6CF A 401 MN A 402 SITE 2 AC3 5 HOH A 501 SITE 1 AC4 1 HIS A 51 SITE 1 AC5 5 ASP A 124 ASP A 314 HOH A 571 HOH A 572 SITE 2 AC5 5 HOH A 573 SITE 1 AC6 6 THR A 101 VAL A 103 ILE A 106 HOH A 504 SITE 2 AC6 6 DG P 9 HOH P 202 SITE 1 AC7 4 GLU A 172 DG T 3 HOH T 204 HOH T 214 SITE 1 AC8 2 DG P 4 HOH P 208 SITE 1 AC9 2 DG D 4 DG D 5 CRYST1 55.084 77.432 55.125 90.00 114.45 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 0.018154 0.000000 0.008254 0.00000 SCALE2 0.000000 0.012915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019928 0.00000