HEADER DNA BINDING PROTEIN/DNA 23-MAY-18 6DIC TITLE D276G DNA POLYMERASE BETA SUBSTRATE COMPLEX WITH TEMPLATING CYTOSINE TITLE 2 AND INCOMING FAPY-DGTP ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*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*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; COMPND 19 MUTATION: 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 ACTIVITY, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,M.R.SMITH,S.H.WILSON,W.A.BEARD REVDAT 4 11-OCT-23 6DIC 1 LINK REVDAT 3 18-DEC-19 6DIC 1 REMARK REVDAT 2 17-APR-19 6DIC 1 JRNL REVDAT 1 30-JAN-19 6DIC 0 JRNL AUTH M.R.SMITH,D.D.SHOCK,W.A.BEARD,M.M.GREENBERG,B.D.FREUDENTHAL, JRNL AUTH 2 S.H.WILSON JRNL TITL A GUARDIAN RESIDUE HINDERS INSERTION OF A FAPY•DGTP JRNL TITL 2 ANALOG BY MODULATING THE OPEN-CLOSED DNA POLYMERASE JRNL TITL 3 TRANSITION. JRNL REF NUCLEIC ACIDS RES. V. 47 3197 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 30649431 JRNL DOI 10.1093/NAR/GKZ002 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 27588 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 2744 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 20.6579 - 5.3760 0.98 1320 139 0.1505 0.1699 REMARK 3 2 5.3760 - 4.2795 0.98 1294 142 0.1287 0.2046 REMARK 3 3 4.2795 - 3.7422 0.99 1315 146 0.1376 0.1643 REMARK 3 4 3.7422 - 3.4017 0.98 1301 123 0.1455 0.1896 REMARK 3 5 3.4017 - 3.1588 0.99 1308 138 0.1773 0.2252 REMARK 3 6 3.1588 - 2.9731 0.98 1272 141 0.2059 0.2768 REMARK 3 7 2.9731 - 2.8246 0.98 1282 151 0.2052 0.2570 REMARK 3 8 2.8246 - 2.7019 0.98 1311 135 0.2005 0.2639 REMARK 3 9 2.7019 - 2.5981 0.98 1267 145 0.2085 0.2647 REMARK 3 10 2.5981 - 2.5086 0.98 1271 133 0.1960 0.2826 REMARK 3 11 2.5086 - 2.4303 0.98 1267 141 0.2069 0.2692 REMARK 3 12 2.4303 - 2.3610 0.97 1274 156 0.2042 0.2571 REMARK 3 13 2.3610 - 2.2989 0.98 1260 152 0.1920 0.2988 REMARK 3 14 2.2989 - 2.2429 0.96 1262 138 0.1981 0.2379 REMARK 3 15 2.2429 - 2.1919 0.96 1248 146 0.2059 0.3443 REMARK 3 16 2.1919 - 2.1453 0.96 1256 133 0.2162 0.2670 REMARK 3 17 2.1453 - 2.1025 0.93 1201 141 0.2059 0.2454 REMARK 3 18 2.1025 - 2.0628 0.93 1189 144 0.2190 0.3003 REMARK 3 19 2.0628 - 2.0260 0.90 1179 116 0.2318 0.3105 REMARK 3 20 2.0260 - 1.9917 0.58 767 84 0.2660 0.3366 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 : 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) : 24.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.87 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6DIC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234641. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-15 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) : 1.54 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27639 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: 2FMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM IMIDAZOLE, 350MM SODIUM ACETATE, REMARK 280 16% PEG3350, PH 8.0, 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 40.20000 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: 5760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -130.0 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 127 CG CD CE NZ REMARK 470 GLU A 129 OE1 OE2 REMARK 470 GLU A 153 CD OE1 OE2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 VAL A 303 CG1 CG2 REMARK 470 LYS A 326 CG CD CE NZ 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. = 2.1 DEGREES REMARK 500 DC T 8 O4' - C1' - N1 ANGL. DEV. = 2.1 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 LYS A 120 10.58 -151.57 REMARK 500 CYS A 178 -139.09 -111.17 REMARK 500 SER A 334 48.93 -93.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH T 157 DISTANCE = 7.12 ANGSTROMS 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 408 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH T 112 O REMARK 620 2 HOH T 121 O 64.5 REMARK 620 3 HOH T 140 O 140.0 75.5 REMARK 620 4 HOH D 213 O 83.0 78.5 92.1 REMARK 620 5 ARG A 126 O 80.2 144.8 139.6 98.6 REMARK 620 6 HOH A 750 O 93.5 98.9 89.9 176.2 81.9 REMARK 620 N 1 2 3 4 5 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 508 O 92.0 REMARK 620 3 THR A 101 O 167.6 80.2 REMARK 620 4 VAL A 103 O 94.0 174.1 93.9 REMARK 620 5 ILE A 106 O 94.9 92.0 94.9 88.0 REMARK 620 6 HOH A 733 O 88.5 93.2 82.5 86.5 173.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 10 O3' REMARK 620 2 ASP A 190 OD1 159.1 REMARK 620 3 ASP A 190 OD2 147.1 51.9 REMARK 620 4 ASP A 192 OD1 83.9 87.1 122.3 REMARK 620 5 ASP A 256 OD2 79.3 119.5 81.5 89.1 REMARK 620 6 GKS A 403 O1A 90.6 69.7 110.0 84.3 168.4 REMARK 620 7 HOH A 630 O 85.5 97.9 73.3 161.8 103.4 81.1 REMARK 620 N 1 2 3 4 5 6 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 DC D 3 OP1 REMARK 620 2 HOH D 202 O 72.0 REMARK 620 3 LYS A 60 O 166.5 96.4 REMARK 620 4 LEU A 62 O 100.1 172.0 91.3 REMARK 620 5 VAL A 65 O 87.9 83.4 83.9 95.6 REMARK 620 6 HOH A 681 O 89.8 101.4 99.4 79.1 173.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 411 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 145 OD1 REMARK 620 2 ASP A 145 OD2 47.1 REMARK 620 3 HOH A 530 O 108.9 79.5 REMARK 620 4 HOH A 661 O 66.0 88.1 70.0 REMARK 620 5 HOH A 738 O 119.8 82.5 86.6 156.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 410 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 O REMARK 620 2 ASP A 190 OD1 70.9 REMARK 620 3 ASP A 192 OD2 92.2 92.4 REMARK 620 4 GKS A 403 O2G 99.9 94.7 167.5 REMARK 620 5 GKS A 403 O2B 136.4 152.4 90.6 78.4 REMARK 620 6 GKS A 403 O1A 145.2 75.1 82.0 89.8 78.2 REMARK 620 7 HOH A 537 O 58.2 129.1 90.5 93.0 78.3 155.2 REMARK 620 N 1 2 3 4 5 6 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 GLU A 249 OE1 REMARK 620 2 GLU A 249 OE2 52.1 REMARK 620 3 HOH A 594 O 153.9 141.5 REMARK 620 4 HOH A 702 O 81.0 75.1 121.2 REMARK 620 5 HOH A 726 O 85.6 130.2 88.2 73.1 REMARK 620 6 HOH A 737 O 127.9 83.1 77.8 60.6 112.0 REMARK 620 7 HOH A 748 O 85.7 129.1 69.5 131.0 58.9 145.9 REMARK 620 N 1 2 3 4 5 6 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 CA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GKS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 411 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6DIA RELATED DB: PDB REMARK 900 RELATED ID: 6MR7 RELATED DB: PDB REMARK 900 RELATED ID: 6MR8 RELATED DB: PDB DBREF 6DIC T 1 16 PDB 6DIC 6DIC 1 16 DBREF 6DIC P 1 10 PDB 6DIC 6DIC 1 10 DBREF 6DIC D 1 5 PDB 6DIC 6DIC 1 5 DBREF 6DIC A 10 335 UNP P06746 DPOLB_HUMAN 10 335 SEQADV 6DIC GLY A 276 UNP P06746 ASP 276 ENGINEERED MUTATION 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 GLY 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 NA A 401 1 HET CA A 402 1 HET GKS A 403 32 HET NA A 404 1 HET CL A 405 1 HET CL A 406 1 HET CL A 407 1 HET NA A 408 1 HET NA A 409 1 HET CA A 410 1 HET CA A 411 1 HETNAM NA SODIUM ION HETNAM CA CALCIUM ION HETNAM GKS 1-[2-AMINO-5-(FORMYLAMINO)-6-OXO-1,6-DIHYDROPYRIMIDIN- HETNAM 2 GKS 4-YL]-2,5-ANHYDRO-1,3-DIDEOXY-6-O-[(R)-HYDROXY{[(R)- HETNAM 3 GKS HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-D- HETNAM 4 GKS RIBO-HEXITOL HETNAM CL CHLORIDE ION FORMUL 5 NA 4(NA 1+) FORMUL 6 CA 3(CA 2+) FORMUL 7 GKS C11 H19 N4 O14 P3 FORMUL 9 CL 3(CL 1-) FORMUL 16 HOH *399(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 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 ASP A 256 N VAL A 193 SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N PHE A 235 O ILE A 257 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 O HOH T 112 NA NA A 408 1556 1555 2.53 LINK O HOH T 121 NA NA A 408 1556 1555 2.48 LINK O HOH T 140 NA NA A 408 1556 1555 2.63 LINK OP1 DG P 9 NA NA A 401 1555 1555 2.53 LINK O3' DC P 10 CA CA A 402 1555 1555 2.42 LINK O HOH P 508 NA NA A 401 1555 1555 2.34 LINK OP1 DC D 3 NA NA A 404 1555 1555 2.40 LINK O HOH D 202 NA NA A 404 1555 1555 2.79 LINK O HOH D 213 NA NA A 408 1556 1555 2.26 LINK O LYS A 60 NA NA A 404 1555 1555 2.53 LINK O LEU A 62 NA NA A 404 1555 1555 2.21 LINK O VAL A 65 NA NA A 404 1555 1555 2.39 LINK O THR A 101 NA NA A 401 1555 1555 2.33 LINK O VAL A 103 NA NA A 401 1555 1555 2.52 LINK O ILE A 106 NA NA A 401 1555 1555 2.44 LINK O ARG A 126 NA NA A 408 1555 1555 2.54 LINK OD1 ASP A 145 CA CA A 411 1555 1555 2.88 LINK OD2 ASP A 145 CA CA A 411 1555 1555 2.52 LINK OD1 ASP A 190 CA CA A 402 1555 1555 2.55 LINK OD2 ASP A 190 CA CA A 402 1555 1555 2.41 LINK O ASP A 190 CA CA A 410 1555 1555 2.86 LINK OD1 ASP A 190 CA CA A 410 1555 1555 2.30 LINK OD1 ASP A 192 CA CA A 402 1555 1555 2.28 LINK OD2 ASP A 192 CA CA A 410 1555 1555 2.29 LINK OE1 GLU A 249 NA NA A 409 1555 1555 2.52 LINK OE2 GLU A 249 NA NA A 409 1555 1555 2.47 LINK OD2 ASP A 256 CA CA A 402 1555 1555 2.23 LINK NA NA A 401 O HOH A 733 1555 1555 2.43 LINK CA CA A 402 O1A GKS A 403 1555 1555 2.48 LINK CA CA A 402 O HOH A 630 1555 1555 2.33 LINK O2G GKS A 403 CA CA A 410 1555 1555 2.33 LINK O2B GKS A 403 CA CA A 410 1555 1555 2.38 LINK O1A GKS A 403 CA CA A 410 1555 1555 2.42 LINK NA NA A 404 O HOH A 681 1555 1555 2.40 LINK NA NA A 408 O HOH A 750 1555 1555 2.67 LINK NA NA A 409 O HOH A 594 1555 1556 2.37 LINK NA NA A 409 O HOH A 702 1555 1555 2.63 LINK NA NA A 409 O HOH A 726 1555 1555 2.31 LINK NA NA A 409 O HOH A 737 1555 1555 2.34 LINK NA NA A 409 O HOH A 748 1555 1555 2.44 LINK CA CA A 410 O HOH A 537 1555 1555 2.41 LINK CA CA A 411 O HOH A 530 1555 1555 2.84 LINK CA CA A 411 O HOH A 661 1555 1555 2.37 LINK CA CA A 411 O HOH A 738 1555 1555 2.34 CISPEP 1 GLY A 274 SER A 275 0 1.79 SITE 1 AC1 6 THR A 101 VAL A 103 ILE A 106 HOH A 733 SITE 2 AC1 6 DG P 9 HOH P 508 SITE 1 AC2 6 ASP A 190 ASP A 192 ASP A 256 GKS A 403 SITE 2 AC2 6 HOH A 630 DC P 10 SITE 1 AC3 28 ARG A 40 GLY A 179 SER A 180 ARG A 183 SITE 2 AC3 28 SER A 188 GLY A 189 ASP A 190 ASP A 192 SITE 3 AC3 28 TYR A 271 PHE A 272 THR A 273 GLY A 274 SITE 4 AC3 28 GLY A 276 ASN A 279 ARG A 283 CA A 402 SITE 5 AC3 28 CA A 410 HOH A 537 HOH A 604 HOH A 613 SITE 6 AC3 28 HOH A 621 HOH A 628 HOH A 630 HOH A 675 SITE 7 AC3 28 HOH A 684 DC P 10 DC T 6 DG T 7 SITE 1 AC4 6 LYS A 60 LEU A 62 VAL A 65 HOH A 681 SITE 2 AC4 6 DC D 3 HOH D 202 SITE 1 AC5 4 GLN A 264 TYR A 266 CYS A 267 HOH A 664 SITE 1 AC6 5 ALA A 32 ILE A 33 HIS A 34 LYS A 35 SITE 2 AC6 5 HOH D 201 SITE 1 AC7 3 ASN A 294 THR A 297 HOH A 747 SITE 1 AC8 6 ARG A 126 HOH A 750 HOH D 213 HOH T 112 SITE 2 AC8 6 HOH T 121 HOH T 140 SITE 1 AC9 6 GLU A 249 HOH A 594 HOH A 702 HOH A 726 SITE 2 AC9 6 HOH A 737 HOH A 748 SITE 1 AD1 4 ASP A 190 ASP A 192 GKS A 403 HOH A 537 SITE 1 AD2 4 ASP A 145 HOH A 530 HOH A 661 HOH A 738 CRYST1 50.800 80.400 55.500 90.00 107.90 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 0.019685 0.000000 0.006358 0.00000 SCALE2 0.000000 0.012438 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018935 0.00000