PDB Short entry for 6MR8 HEADER DNA BINDING PROTEIN/DNA 11-OCT-18 6MR8 TITLE D276G DNA POLYMERASE BETA SUBSTRATE COMPLEX WITH TEMPLATING ADENINE TITLE 2 AND 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 EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,M.R.SMITH,S.H.WILSON,W.A.BEARD REVDAT 4 11-OCT-23 6MR8 1 LINK REVDAT 3 18-DEC-19 6MR8 1 REMARK REVDAT 2 17-APR-19 6MR8 1 JRNL REVDAT 1 30-JAN-19 6MR8 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. 1.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 65469 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.670 REMARK 3 FREE R VALUE TEST SET COUNT : 3712 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 24.7976 - 5.6698 0.95 2336 144 0.1595 0.1733 REMARK 3 2 5.6698 - 4.5091 0.97 2399 142 0.1608 0.1835 REMARK 3 3 4.5091 - 3.9417 0.97 2389 140 0.1554 0.1688 REMARK 3 4 3.9417 - 3.5825 0.98 2439 143 0.1679 0.2167 REMARK 3 5 3.5825 - 3.3263 0.98 2420 143 0.1654 0.1952 REMARK 3 6 3.3263 - 3.1306 0.98 2432 140 0.2001 0.2387 REMARK 3 7 3.1306 - 2.9741 0.97 2388 152 0.2186 0.2857 REMARK 3 8 2.9741 - 2.8448 0.96 2398 140 0.2309 0.3209 REMARK 3 9 2.8448 - 2.7355 0.97 2363 136 0.2233 0.2709 REMARK 3 10 2.7355 - 2.6412 0.97 2374 144 0.2185 0.2591 REMARK 3 11 2.6412 - 2.5587 0.97 2421 153 0.2266 0.3084 REMARK 3 12 2.5587 - 2.4856 0.97 2377 132 0.2158 0.2825 REMARK 3 13 2.4856 - 2.4202 0.97 2351 144 0.2190 0.3209 REMARK 3 14 2.4202 - 2.3612 0.97 2409 142 0.2195 0.3123 REMARK 3 15 2.3612 - 2.3076 0.96 2348 139 0.2151 0.2420 REMARK 3 16 2.3076 - 2.2585 0.96 2365 147 0.2099 0.2247 REMARK 3 17 2.2585 - 2.2134 0.95 2331 143 0.2089 0.3069 REMARK 3 18 2.2134 - 2.1716 0.95 2318 129 0.2218 0.3037 REMARK 3 19 2.1716 - 2.1329 0.93 2318 144 0.2242 0.2888 REMARK 3 20 2.1329 - 2.0967 0.92 2248 139 0.2288 0.3195 REMARK 3 21 2.0967 - 2.0629 0.90 2226 127 0.2324 0.2505 REMARK 3 22 2.0629 - 2.0312 0.87 2104 138 0.2307 0.2393 REMARK 3 23 2.0312 - 2.0013 0.87 2163 130 0.2438 0.2866 REMARK 3 24 2.0013 - 1.9732 0.84 2025 126 0.2514 0.3011 REMARK 3 25 1.9732 - 1.9465 0.83 2084 124 0.2990 0.2844 REMARK 3 26 1.9465 - 1.9212 0.80 1955 126 0.3270 0.3469 REMARK 3 27 1.9212 - 1.8972 0.72 1776 105 0.3573 0.3081 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.16 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 6MR8 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_1000237349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-AUG-18 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 : 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 : 65523 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.897 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.83100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 3ISB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, PH 8.0, 18% 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 40.14100 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: 5070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 10 REMARK 465 THR A 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 ASN A 245 REMARK 465 ASP A 246 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 48 CG CD CE NZ REMARK 470 LYS A 87 CD CE NZ REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 280 CG CD CE NZ REMARK 470 GLU A 295 CG CD OE1 OE2 REMARK 470 LYS A 326 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 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. = 2.5 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 ASN A 12 28.45 -151.33 REMARK 500 CYS A 178 -141.22 -108.31 REMARK 500 ASN A 294 -167.62 -128.41 REMARK 500 ASP A 332 30.48 -97.70 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 THR A 101 O REMARK 620 2 VAL A 103 O 91.7 REMARK 620 3 ILE A 106 O 93.1 86.7 REMARK 620 4 HOH A 694 O 83.6 93.5 176.7 REMARK 620 5 DG P 9 OP1 169.2 96.6 94.2 89.0 REMARK 620 6 HOH P 204 O 83.2 172.4 88.0 91.5 89.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 408 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 145 OD1 REMARK 620 2 ASP A 145 OD2 51.4 REMARK 620 3 HOH A 550 O 118.3 76.1 REMARK 620 4 HOH A 666 O 114.2 73.2 70.0 REMARK 620 5 HOH A 677 O 75.1 89.5 74.3 143.0 REMARK 620 6 HOH A 717 O 156.5 152.0 81.5 83.5 100.6 REMARK 620 7 HOH T 204 O 82.7 102.3 145.7 76.7 139.8 86.8 REMARK 620 8 HOH T 210 O 79.9 130.2 148.4 128.8 87.3 76.8 55.7 REMARK 620 N 1 2 3 4 5 6 7 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 GLU A 172 OE1 REMARK 620 2 GLU A 172 OE2 43.8 REMARK 620 3 HOH A 699 O 77.2 72.0 REMARK 620 4 HOH A 706 O 73.9 91.2 150.4 REMARK 620 5 HOH A 713 O 73.9 110.1 65.2 100.0 REMARK 620 6 HOH T 237 O 105.1 148.3 112.2 69.9 52.2 REMARK 620 7 HOH D 111 O 141.6 131.5 68.1 136.1 76.8 74.6 REMARK 620 8 HOH D 112 O 127.3 83.9 94.6 108.0 148.4 125.5 73.0 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 406 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 91.5 REMARK 620 3 GKS A 401 O1A 167.4 87.8 REMARK 620 4 GKS A 401 O2A 136.0 116.7 54.2 REMARK 620 5 HOH A 512 O 82.2 80.5 110.0 71.1 REMARK 620 6 HOH A 662 O 69.6 74.4 98.2 147.2 141.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 240 OE1 REMARK 620 2 GLU A 288 OE1 19.1 REMARK 620 3 GLU A 288 OE2 21.4 2.3 REMARK 620 4 HOH A 566 O 23.1 4.0 1.8 REMARK 620 5 HOH A 620 O 23.1 4.1 1.8 1.5 REMARK 620 6 HOH A 649 O 18.3 1.8 3.6 4.9 5.4 REMARK 620 7 HOH A 660 O 20.4 2.2 2.0 3.7 3.0 3.9 REMARK 620 8 HOH A 704 O 22.0 4.1 3.2 2.6 4.1 3.9 5.0 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 407 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GKS A 401 O1G REMARK 620 2 GKS A 401 O3B 50.9 REMARK 620 3 GKS A 401 O3A 105.3 55.3 REMARK 620 4 GKS A 401 O2A 162.7 111.9 57.5 REMARK 620 5 HOH A 537 O 128.5 166.4 125.9 68.6 REMARK 620 6 HOH A 689 O 69.4 118.3 172.2 127.6 59.1 REMARK 620 7 HOH A 703 O 65.9 85.7 99.9 115.1 106.6 83.3 REMARK 620 8 HOH P 235 O 110.3 152.0 130.7 84.6 40.1 57.1 66.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 607 O REMARK 620 2 HOH A 734 O 99.8 REMARK 620 3 HOH A 743 O 64.1 110.9 REMARK 620 4 HOH P 208 O 135.3 100.2 71.4 REMARK 620 5 HOH P 212 O 86.0 161.4 87.6 87.5 REMARK 620 N 1 2 3 4 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 HOH T 209 O REMARK 620 2 HOH T 230 O 70.0 REMARK 620 3 HOH T 252 O 86.7 147.8 REMARK 620 4 HOH D 102 O 125.4 81.8 130.3 REMARK 620 5 HOH D 118 O 68.1 93.0 98.7 67.8 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 NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA 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 CA A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA T 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO P 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6DIC RELATED DB: PDB REMARK 900 RELATED ID: 6DIA RELATED DB: PDB REMARK 900 RELATED ID: 6MR7 RELATED DB: PDB DBREF 6MR8 A 11 335 UNP P06746 DPOLB_HUMAN 11 335 DBREF 6MR8 T 1 16 PDB 6MR8 6MR8 1 16 DBREF 6MR8 P 1 10 PDB 6MR8 6MR8 1 10 DBREF 6MR8 D 1 5 PDB 6MR8 6MR8 1 5 SEQADV 6MR8 GLY A 276 UNP P06746 ASP 276 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 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 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 32 HET NA A 402 1 HET NA A 403 1 HET NA A 404 1 HET NA A 405 1 HET CA A 406 1 HET CA A 407 1 HET CA A 408 1 HET NA T 101 1 HET EDO P 101 10 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 NA SODIUM ION HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 GKS C11 H19 N4 O14 P3 FORMUL 6 NA 5(NA 1+) FORMUL 10 CA 3(CA 2+) FORMUL 14 EDO C2 H6 O2 FORMUL 15 HOH *370(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 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 THR A 101 NA NA A 404 1555 1555 2.32 LINK O VAL A 103 NA NA A 404 1555 1555 2.45 LINK O ILE A 106 NA NA A 404 1555 1555 2.40 LINK OD1 ASP A 145 CA CA A 408 1555 1555 2.48 LINK OD2 ASP A 145 CA CA A 408 1555 1555 2.59 LINK OE1 GLU A 172 NA NA A 405 1555 1555 3.08 LINK OE2 GLU A 172 NA NA A 405 1555 1555 2.71 LINK OD1 ASP A 190 CA CA A 406 1555 1555 2.47 LINK OD2AASP A 192 CA CA A 406 1555 1555 2.32 LINK OE1 GLN A 240 NA NA A 403 1555 1655 2.40 LINK OE1 GLU A 288 NA NA A 403 1555 1555 3.13 LINK OE2 GLU A 288 NA NA A 403 1555 1555 3.05 LINK O1A GKS A 401 CA CA A 406 1555 1555 2.28 LINK O2A GKS A 401 CA CA A 406 1555 1555 3.15 LINK O1G GKS A 401 CA CA A 407 1555 1555 2.65 LINK O3B GKS A 401 CA CA A 407 1555 1555 3.12 LINK O3A GKS A 401 CA CA A 407 1555 1555 2.58 LINK O2A GKS A 401 CA CA A 407 1555 1555 2.68 LINK NA NA A 402 O HOH A 607 1555 1555 2.52 LINK NA NA A 402 O HOH A 734 1555 1555 2.36 LINK NA NA A 402 O HOH A 743 1555 1555 2.97 LINK NA NA A 402 O HOH P 208 1555 1555 2.34 LINK NA NA A 402 O HOH P 212 1555 1555 2.82 LINK NA NA A 403 O HOH A 566 1555 1555 2.11 LINK NA NA A 403 O HOH A 620 1555 1455 2.74 LINK NA NA A 403 O HOH A 649 1555 1555 2.86 LINK NA NA A 403 O HOH A 660 1555 1555 2.37 LINK NA NA A 403 O HOH A 704 1555 1455 2.69 LINK NA NA A 404 O HOH A 694 1555 1555 2.37 LINK NA NA A 404 OP1 DG P 9 1555 1555 2.29 LINK NA NA A 404 O HOH P 204 1555 1555 2.60 LINK NA NA A 405 O HOH A 699 1555 1555 2.98 LINK NA NA A 405 O HOH A 706 1555 1555 2.09 LINK NA NA A 405 O HOH A 713 1555 1555 2.61 LINK NA NA A 405 O HOH T 237 1555 1554 2.51 LINK NA NA A 405 O HOH D 111 1555 1554 2.38 LINK NA NA A 405 O HOH D 112 1555 1554 2.62 LINK CA CA A 406 O HOH A 512 1555 1555 2.23 LINK CA CA A 406 O HOH A 662 1555 1555 2.69 LINK CA CA A 407 O HOH A 537 1555 1555 2.65 LINK CA CA A 407 O HOH A 689 1555 1555 2.81 LINK CA CA A 407 O HOH A 703 1555 1555 3.14 LINK CA CA A 407 O BHOH P 235 1555 1555 3.12 LINK CA CA A 408 O HOH A 550 1555 1555 2.67 LINK CA CA A 408 O HOH A 666 1555 1555 2.35 LINK CA CA A 408 O HOH A 677 1555 1555 2.50 LINK CA CA A 408 O HOH A 717 1555 1555 2.40 LINK CA CA A 408 O HOH T 204 1555 2656 2.57 LINK CA CA A 408 O HOH T 210 1555 2656 2.58 LINK NA NA T 101 O HOH T 209 1555 1555 2.35 LINK NA NA T 101 O HOH T 230 1555 1555 2.63 LINK NA NA T 101 O HOH T 252 1555 1555 2.11 LINK NA NA T 101 O HOH D 102 1555 1555 2.56 LINK NA NA T 101 O HOH D 118 1555 1555 2.67 CISPEP 1 GLY A 274 SER A 275 0 0.75 SITE 1 AC1 19 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC1 19 GLY A 189 ASP A 192 TYR A 271 PHE A 272 SITE 3 AC1 19 GLY A 276 CA A 406 CA A 407 HOH A 501 SITE 4 AC1 19 HOH A 537 HOH A 564 HOH A 597 HOH A 683 SITE 5 AC1 19 DC P 10 DA T 6 DG T 7 SITE 1 AC2 5 HOH A 607 HOH A 734 HOH A 743 HOH P 208 SITE 2 AC2 5 HOH P 212 SITE 1 AC3 7 GLN A 240 GLU A 288 HOH A 566 HOH A 620 SITE 2 AC3 7 HOH A 649 HOH A 660 HOH A 704 SITE 1 AC4 6 THR A 101 VAL A 103 ILE A 106 HOH A 694 SITE 2 AC4 6 DG P 9 HOH P 204 SITE 1 AC5 7 GLU A 172 HOH A 699 HOH A 706 HOH A 713 SITE 2 AC5 7 HOH D 111 HOH D 112 HOH T 237 SITE 1 AC6 6 ASP A 190 ASP A 192 GKS A 401 CA A 407 SITE 2 AC6 6 HOH A 512 HOH A 662 SITE 1 AC7 4 GKS A 401 CA A 406 HOH A 537 HOH A 689 SITE 1 AC8 5 ASP A 145 HOH A 550 HOH A 666 HOH A 677 SITE 2 AC8 5 HOH A 717 SITE 1 AC9 5 HOH D 102 HOH D 118 HOH T 209 HOH T 230 SITE 2 AC9 5 HOH T 252 SITE 1 AD1 5 DG P 7 DC P 8 HOH P 227 DA T 11 SITE 2 AD1 5 DT T 12 CRYST1 55.015 80.282 55.564 90.00 110.46 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 0.018177 0.000000 0.006781 0.00000 SCALE2 0.000000 0.012456 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019209 0.00000