HEADER DNA BINDING PROTEIN/DNA 11-OCT-18 6MR7 TITLE DNA POLYMERASE BETA SUBSTRATE COMPLEX WITH TEMPLATING ADENINE AND TITLE 2 INCOMING FAPY-DGTP 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 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*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*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 ACTIVITY, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX, DNA POLYMERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,M.R.SMITH,S.H.WILSON,W.A.BEARD REVDAT 4 11-OCT-23 6MR7 1 LINK REVDAT 3 18-DEC-19 6MR7 1 REMARK REVDAT 2 17-APR-19 6MR7 1 JRNL REVDAT 1 30-JAN-19 6MR7 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. 2.14 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) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 43797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.180 REMARK 3 FREE R VALUE TEST SET COUNT : 3584 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 24.7126 - 6.3173 0.88 1518 129 0.1605 0.1799 REMARK 3 2 6.3173 - 5.0281 0.93 1582 130 0.1614 0.2092 REMARK 3 3 5.0281 - 4.3966 0.93 1603 139 0.1481 0.1618 REMARK 3 4 4.3966 - 3.9964 0.93 1586 145 0.1455 0.1875 REMARK 3 5 3.9964 - 3.7110 0.94 1615 140 0.1541 0.1992 REMARK 3 6 3.7110 - 3.4928 0.94 1572 150 0.1571 0.2361 REMARK 3 7 3.4928 - 3.3183 0.93 1619 146 0.1613 0.2423 REMARK 3 8 3.3183 - 3.1742 0.94 1617 139 0.1772 0.2716 REMARK 3 9 3.1742 - 3.0522 0.92 1579 137 0.2212 0.2970 REMARK 3 10 3.0522 - 2.9471 0.92 1587 146 0.2247 0.2916 REMARK 3 11 2.9471 - 2.8551 0.93 1548 141 0.2276 0.3891 REMARK 3 12 2.8551 - 2.7736 0.93 1603 138 0.2302 0.3631 REMARK 3 13 2.7736 - 2.7007 0.93 1610 153 0.2249 0.3180 REMARK 3 14 2.7007 - 2.6348 0.91 1523 130 0.2246 0.2911 REMARK 3 15 2.6348 - 2.5750 0.92 1618 151 0.2265 0.2975 REMARK 3 16 2.5750 - 2.5203 0.91 1495 142 0.2125 0.3685 REMARK 3 17 2.5203 - 2.4699 0.92 1620 143 0.2228 0.2721 REMARK 3 18 2.4699 - 2.4233 0.92 1539 130 0.2187 0.3093 REMARK 3 19 2.4233 - 2.3801 0.91 1576 144 0.2296 0.3268 REMARK 3 20 2.3801 - 2.3398 0.90 1549 135 0.2335 0.2809 REMARK 3 21 2.3398 - 2.3021 0.89 1494 139 0.2445 0.3458 REMARK 3 22 2.3021 - 2.2667 0.87 1510 125 0.2319 0.3335 REMARK 3 23 2.2667 - 2.2333 0.86 1492 128 0.2344 0.3414 REMARK 3 24 2.2333 - 2.2019 0.86 1444 124 0.2545 0.3079 REMARK 3 25 2.2019 - 2.1722 0.86 1492 140 0.2449 0.3115 REMARK 3 26 2.1722 - 2.1440 0.72 1222 120 0.2479 0.3194 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.72 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 6MR7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000236892. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-18 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 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R 200K-A REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24393 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 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) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.41500 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: PHASER REMARK 200 STARTING MODEL: 3ISB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE PH 7.5, 16% PEG3350, REMARK 280 AND 350 MM SODIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K 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 39.91250 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: 5240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 PRO A 208 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 THR A 10 OG1 CG2 REMARK 470 LYS A 48 CD CE NZ REMARK 470 ARG A 83 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 120 CE NZ REMARK 470 GLU A 129 CG CD OE1 OE2 REMARK 470 GLU A 153 CG CD OE1 OE2 REMARK 470 GLU A 186 CG CD OE1 OE2 REMARK 470 GLU A 203 CG CD OE1 OE2 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 GLU A 247 CG CD OE1 OE2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 289 CD CE NZ REMARK 470 GLN A 324 CD OE1 NE2 REMARK 470 LYS A 326 CG CD CE NZ 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: 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 T 2 O3' DC T 2 C3' -0.037 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. = 2.0 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 CYS A 178 -142.07 -106.02 REMARK 500 GLU A 203 46.31 -104.74 REMARK 500 ARG A 333 35.35 -93.10 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 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 89.7 REMARK 620 3 VAL A 65 O 90.6 101.1 REMARK 620 4 HOH A 643 O 87.7 79.4 178.2 REMARK 620 5 DC D 3 OP1 173.8 93.4 94.0 87.7 REMARK 620 6 HOH D 106 O 92.1 170.2 88.6 91.0 84.0 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 THR A 101 O REMARK 620 2 VAL A 103 O 90.0 REMARK 620 3 ILE A 106 O 92.0 83.4 REMARK 620 4 DG P 9 OP1 172.8 94.3 94.1 REMARK 620 5 HOH P 103 O 85.2 171.4 89.5 91.1 REMARK 620 6 HOH P 121 O 88.4 93.9 177.2 85.6 93.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 145 OD1 REMARK 620 2 ASP A 145 OD2 49.4 REMARK 620 3 HOH A 535 O 117.7 78.9 REMARK 620 4 HOH A 634 O 71.8 98.0 86.5 REMARK 620 5 HOH A 652 O 103.8 72.9 87.8 170.1 REMARK 620 6 HOH A 661 O 156.1 149.0 85.8 107.8 79.9 REMARK 620 7 HOH A 673 O 78.3 127.5 132.7 54.8 133.9 82.3 REMARK 620 8 HOH T 223 O 86.5 94.5 136.1 137.2 49.5 78.1 85.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA T 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 172 OE1 REMARK 620 2 GLU A 172 OE2 46.1 REMARK 620 3 HOH A 576 O 45.5 72.3 REMARK 620 4 HOH A 645 O 45.8 74.7 3.3 REMARK 620 5 HOH T 220 O 46.3 76.0 4.8 1.5 REMARK 620 6 HOH T 227 O 43.2 73.2 4.4 2.7 3.2 REMARK 620 7 HOH D 110 O 46.9 74.5 2.3 1.9 3.1 4.3 REMARK 620 8 HOH D 111 O 44.1 72.1 1.7 2.7 4.1 2.7 2.9 REMARK 620 N 1 2 3 4 5 6 7 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 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 91.0 REMARK 620 3 GKS A 401 O2G 92.5 168.8 REMARK 620 4 GKS A 401 O2G 90.0 164.6 5.3 REMARK 620 5 GKS A 401 O2B 139.3 96.5 74.0 73.1 REMARK 620 6 GKS A 401 O2B 142.7 96.8 74.1 73.5 3.5 REMARK 620 7 GKS A 401 O1A 150.8 82.8 99.1 103.4 69.9 66.5 REMARK 620 8 GKS A 401 O1A 159.4 83.8 96.5 100.3 61.2 57.9 8.7 REMARK 620 9 HOH A 515 O 79.3 100.5 90.6 94.7 137.4 134.0 73.9 82.1 REMARK 620 N 1 2 3 4 5 6 7 8 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 ASP A 190 OD2 REMARK 620 2 GKS A 401 O2G 90.4 REMARK 620 3 GKS A 401 O2G 88.0 3.9 REMARK 620 4 HOH A 501 O 130.2 49.9 53.6 REMARK 620 5 HOH A 515 O 47.1 70.2 70.7 87.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GKS 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 CA 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 NA 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 EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA T 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6DIA RELATED DB: PDB REMARK 900 RELATED ID: 6DIC RELATED DB: PDB REMARK 900 RELATED ID: 6MR8 RELATED DB: PDB DBREF 6MR7 A 10 335 UNP P06746 DPOLB_HUMAN 10 335 DBREF 6MR7 T 1 16 PDB 6MR7 6MR7 1 16 DBREF 6MR7 P 1 10 PDB 6MR7 6MR7 1 10 DBREF 6MR7 D 1 5 PDB 6MR7 6MR7 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 DA 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 HET GKS A 401 64 HET CA A 402 1 HET CA A 403 1 HET NA A 404 1 HET NA A 405 1 HET NA A 406 1 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET NA T 101 1 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 CA CALCIUM ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 GKS C11 H19 N4 O14 P3 FORMUL 6 CA 2(CA 2+) FORMUL 8 NA 4(NA 1+) FORMUL 11 EDO 4(C2 H6 O2) FORMUL 16 HOH *286(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 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 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 ARG A 258 N LEU A 195 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 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 LYS A 60 NA NA A 404 1555 1555 2.46 LINK O LEU A 62 NA NA A 404 1555 1555 2.35 LINK O VAL A 65 NA NA A 404 1555 1555 2.28 LINK O THR A 101 NA NA A 405 1555 1555 2.29 LINK O VAL A 103 NA NA A 405 1555 1555 2.45 LINK O ILE A 106 NA NA A 405 1555 1555 2.44 LINK OD1 ASP A 145 CA CA A 403 1555 1555 2.68 LINK OD2 ASP A 145 CA CA A 403 1555 1555 2.64 LINK OE1 GLU A 172 NA NA T 101 1555 1554 2.84 LINK OE2 GLU A 172 NA NA T 101 1555 1554 2.80 LINK OD1 ASP A 190 CA CA A 402 1555 1555 2.40 LINK OD2 ASP A 190 NA NA A 406 1555 1555 2.93 LINK OD2 ASP A 192 CA CA A 402 1555 1555 2.35 LINK O2GAGKS A 401 CA CA A 402 1555 1555 2.45 LINK O2GBGKS A 401 CA CA A 402 1555 1555 2.41 LINK O2BAGKS A 401 CA CA A 402 1555 1555 2.70 LINK O2BBGKS A 401 CA CA A 402 1555 1555 2.75 LINK O1AAGKS A 401 CA CA A 402 1555 1555 2.63 LINK O1ABGKS A 401 CA CA A 402 1555 1555 2.43 LINK O2GAGKS A 401 NA NA A 406 1555 1555 2.66 LINK O2GBGKS A 401 NA NA A 406 1555 1555 2.79 LINK CA CA A 402 O HOH A 515 1555 1555 2.31 LINK CA CA A 402 O HOH A 603 1555 1555 2.59 LINK CA CA A 403 O HOH A 535 1555 1555 2.45 LINK CA CA A 403 O HOH A 634 1555 1555 2.53 LINK CA CA A 403 O HOH A 652 1555 1555 2.76 LINK CA CA A 403 O HOH A 661 1555 1555 2.43 LINK CA CA A 403 O HOH A 673 1555 1555 2.72 LINK CA CA A 403 O HOH T 223 1555 2856 2.75 LINK NA NA A 404 O HOH A 643 1555 1555 2.60 LINK NA NA A 404 OP1 DC D 3 1555 1555 2.89 LINK NA NA A 404 O HOH D 106 1555 1555 2.24 LINK NA NA A 405 OP1 DG P 9 1555 1555 2.28 LINK NA NA A 405 O HOH P 103 1555 1555 2.53 LINK NA NA A 405 O HOH P 121 1555 1555 2.61 LINK NA NA A 406 O HOH A 501 1555 1555 2.57 LINK NA NA A 406 O HOH A 515 1555 1555 3.18 LINK O HOH A 576 NA NA T 101 1556 1555 2.80 LINK O HOH A 645 NA NA T 101 1556 1555 2.44 LINK NA NA T 101 O HOH T 220 1555 1555 2.58 LINK NA NA T 101 O HOH T 227 1555 1555 2.30 LINK NA NA T 101 O HOH D 110 1555 1555 2.36 LINK NA NA T 101 O HOH D 111 1555 1555 2.74 CISPEP 1 GLY A 274 SER A 275 0 -1.22 SITE 1 AC1 26 GLY A 179 SER A 180 ARG A 183 SER A 188 SITE 2 AC1 26 GLY A 189 ASP A 190 ASP A 192 ARG A 258 SITE 3 AC1 26 TYR A 271 PHE A 272 GLY A 274 SER A 275 SITE 4 AC1 26 ASP A 276 ASN A 279 CA A 402 NA A 406 SITE 5 AC1 26 EDO A 409 HOH A 501 HOH A 505 HOH A 507 SITE 6 AC1 26 HOH A 515 HOH A 560 HOH A 602 HOH A 603 SITE 7 AC1 26 DC P 10 DA T 6 SITE 1 AC2 5 ASP A 190 ASP A 192 GKS A 401 HOH A 515 SITE 2 AC2 5 HOH A 603 SITE 1 AC3 6 ASP A 145 HOH A 535 HOH A 634 HOH A 652 SITE 2 AC3 6 HOH A 661 HOH A 673 SITE 1 AC4 6 LYS A 60 LEU A 62 VAL A 65 HOH A 643 SITE 2 AC4 6 DC D 3 HOH D 106 SITE 1 AC5 6 THR A 101 VAL A 103 ILE A 106 DG P 9 SITE 2 AC5 6 HOH P 103 HOH P 121 SITE 1 AC6 4 ASP A 190 GKS A 401 EDO A 410 HOH A 501 SITE 1 AC7 6 GLY A 118 PRO A 312 ASP A 314 ASP A 318 SITE 2 AC7 6 EDO A 408 HOH A 510 SITE 1 AC8 5 ASP A 124 ASP A 314 ASP A 318 EDO A 407 SITE 2 AC8 5 HOH A 510 SITE 1 AC9 4 TYR A 271 GLU A 295 GKS A 401 DC T 8 SITE 1 AD1 7 PHE A 146 GLY A 189 NA A 406 HOH A 512 SITE 2 AD1 7 HOH A 612 HOH P 102 HOH P 105 SITE 1 AD2 7 GLU A 172 HOH A 576 HOH A 645 HOH D 110 SITE 2 AD2 7 HOH D 111 HOH T 220 HOH T 227 CRYST1 55.032 79.825 55.518 90.00 110.60 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 0.018171 0.000000 0.006829 0.00000 SCALE2 0.000000 0.012527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019242 0.00000