HEADER TRANSCRIPTION/DNA 16-MAR-18 6CR3 TITLE TERNARY COMPLEX CRYSTAL STRUCTURE OF DNA POLYMERASE BETA WITH A TITLE 2 DIDEOXY TERMINATED PRIMER WITH CBR2, BETA, GAMMA DATP ANALOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*TP*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*(DOC))-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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: POLB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: TAP56; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PWL-11; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 MOL_ID: 4; SOURCE 19 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 20 ORGANISM_COMMON: HUMAN; SOURCE 21 ORGANISM_TAXID: 9606; SOURCE 22 GENE: POLB; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 25 EXPRESSION_SYSTEM_STRAIN: TAP56; SOURCE 26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 27 EXPRESSION_SYSTEM_PLASMID: PWL-11 KEYWDS DNA POLYMERASE BETA, CONFORMATIONAL CHANGE, ENZYME MECHANISM, LFER, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.K.BATRA,S.H.WILSON REVDAT 3 04-OCT-23 6CR3 1 LINK REVDAT 2 11-JUL-18 6CR3 1 JRNL REVDAT 1 27-JUN-18 6CR3 0 JRNL AUTH V.K.BATRA,K.OERTELL,W.A.BEARD,B.A.KASHEMIROV,C.E.MCKENNA, JRNL AUTH 2 M.F.GOODMAN,S.H.WILSON JRNL TITL MAPPING FUNCTIONAL SUBSTRATE-ENZYME INTERACTIONS IN THE POL JRNL TITL 2 BETA ACTIVE SITE THROUGH CHEMICAL BIOLOGY: STRUCTURAL JRNL TITL 3 RESPONSES TO ACIDITY MODIFICATION OF INCOMING DNTPS. JRNL REF BIOCHEMISTRY V. 57 3934 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 29874056 JRNL DOI 10.1021/ACS.BIOCHEM.8B00418 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 30442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.550 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 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 23.1836 - 4.6807 1.00 2115 149 0.1485 0.1595 REMARK 3 2 4.6807 - 3.7201 1.00 2083 144 0.1346 0.1891 REMARK 3 3 3.7201 - 3.2513 1.00 2080 145 0.1428 0.1948 REMARK 3 4 3.2513 - 2.9547 1.00 2073 145 0.1963 0.2566 REMARK 3 5 2.9547 - 2.7433 0.99 2072 146 0.2019 0.2443 REMARK 3 6 2.7433 - 2.5818 1.00 2078 146 0.1990 0.2460 REMARK 3 7 2.5818 - 2.4526 1.00 2058 145 0.1927 0.2846 REMARK 3 8 2.4526 - 2.3460 1.00 2032 143 0.1945 0.2438 REMARK 3 9 2.3460 - 2.2557 1.00 2082 146 0.1981 0.2633 REMARK 3 10 2.2557 - 2.1780 1.00 2090 146 0.1966 0.2768 REMARK 3 11 2.1780 - 2.1099 1.00 2042 143 0.1974 0.2670 REMARK 3 12 2.1099 - 2.0496 1.00 2066 146 0.2123 0.2665 REMARK 3 13 2.0496 - 1.9957 0.96 1964 138 0.2270 0.2794 REMARK 3 14 1.9957 - 1.9470 0.77 1612 113 0.2633 0.3292 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.46 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 : 0.007 3400 REMARK 3 ANGLE : 0.877 4715 REMARK 3 CHIRALITY : 0.048 514 REMARK 3 PLANARITY : 0.005 496 REMARK 3 DIHEDRAL : 18.034 1941 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 6CR3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000233076. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5, 50 MM IMIDAZOLE, 350 MM REMARK 200 SODIUM ACETATE 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30503 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.57900 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 (%): 46.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16-18% PEG 3350, VAPOR DIFFUSION, REMARK 280 SITTING DROP, 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 39.83450 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: 5730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 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 LEU A 70 CG CD1 CD2 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 O HOH A 888 O HOH A 894 1.83 REMARK 500 O HOH A 519 O HOH A 610 1.90 REMARK 500 O HOH A 764 O HOH A 842 1.92 REMARK 500 OP2 DG P 7 O HOH P 101 1.95 REMARK 500 O HOH A 539 O HOH A 798 2.00 REMARK 500 O HOH A 801 O HOH A 874 2.00 REMARK 500 OE1 GLU A 216 O HOH A 501 2.03 REMARK 500 O HOH A 849 O HOH A 875 2.04 REMARK 500 O HOH A 833 O HOH A 843 2.04 REMARK 500 ND1 HIS A 285 O HOH A 502 2.05 REMARK 500 O5' DOC P 10 O HOH P 102 2.06 REMARK 500 O HOH A 729 O HOH A 807 2.13 REMARK 500 O HOH A 804 O HOH A 820 2.14 REMARK 500 O HOH A 724 O HOH A 823 2.14 REMARK 500 O HOH A 718 O HOH A 782 2.15 REMARK 500 O HOH A 782 O HOH A 861 2.15 REMARK 500 O HOH A 761 O HOH A 859 2.15 REMARK 500 O HOH A 585 O HOH A 866 2.17 REMARK 500 O4 DT P 3 O HOH P 103 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 726 O HOH A 886 1455 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 8 O3' DC T 8 C3' -0.041 REMARK 500 DG D 1 P DG D 1 OP3 -0.116 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 -138.09 -115.60 REMARK 500 ASP A 246 -7.57 71.09 REMARK 500 ASN A 294 -167.30 -127.69 REMARK 500 THR A 304 0.60 -68.84 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 A 895 DISTANCE = 5.91 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 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 HOH P 106 O 86.7 REMARK 620 3 THR A 101 O 164.8 83.0 REMARK 620 4 VAL A 103 O 96.6 176.6 93.9 REMARK 620 5 ILE A 106 O 97.0 89.5 94.1 89.3 REMARK 620 6 HOH A 803 O 87.8 94.3 81.8 86.7 174.0 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 HOH P 102 O REMARK 620 2 ASP A 190 OD1 112.0 REMARK 620 3 ASP A 190 OD2 81.9 43.4 REMARK 620 4 ASP A 192 OD1 165.3 71.9 108.2 REMARK 620 5 ASP A 256 OD2 91.8 128.4 101.3 96.4 REMARK 620 6 H84 A 401 O1A 83.0 63.9 89.1 86.4 167.6 REMARK 620 N 1 2 3 4 5 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 104 O 77.7 REMARK 620 3 LYS A 60 O 172.1 94.5 REMARK 620 4 LEU A 62 O 91.4 164.7 96.2 REMARK 620 5 VAL A 65 O 90.0 91.9 90.6 98.8 REMARK 620 6 HOH A 557 O 90.6 91.8 89.3 77.5 176.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 96.0 REMARK 620 3 H84 A 401 O1A 97.3 89.8 REMARK 620 4 H84 A 401 O1G 84.8 175.4 85.6 REMARK 620 5 H84 A 401 O1B 167.0 90.6 93.9 89.5 REMARK 620 6 HOH A 554 O 82.5 91.0 179.1 93.6 86.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue H84 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG 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 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 DBREF 6CR3 T 1 16 PDB 6CR3 6CR3 1 16 DBREF 6CR3 P 1 10 PDB 6CR3 6CR3 1 10 DBREF 6CR3 D 1 5 PDB 6CR3 6CR3 1 5 DBREF 6CR3 A 1 335 UNP P06746 DPOLB_HUMAN 1 335 SEQADV 6CR3 LEU A 70 UNP P06746 ALA 70 CONFLICT SEQRES 1 T 16 DC DC DG DA DC DT 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 DOC 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 LEU GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU HET DOC P 10 18 HET H84 A 401 32 HET MG A 402 1 HET NA A 403 1 HET NA A 404 1 HET NA A 405 1 HET CL A 406 1 HET CL A 407 1 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM H84 2'-DEOXY-5'-O-[(R)-{[(R)-[DIBROMO(PHOSPHONO) HETNAM 2 H84 METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY) HETNAM 3 H84 PHOSPHORYL]ADENOSINE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN H84 BETA, GAMMA DATP ANALOGUE FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 5 H84 C11 H16 BR2 N5 O11 P3 FORMUL 6 MG MG 2+ FORMUL 7 NA 3(NA 1+) FORMUL 10 CL 2(CL 1-) FORMUL 12 HOH *499(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 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 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 LEU A 228 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 O3' DG P 9 P DOC P 10 1555 1555 1.60 LINK OP1 DG P 9 NA NA A 403 1555 1555 2.43 LINK O HOH P 102 NA NA A 405 1555 1555 2.22 LINK O HOH P 106 NA NA A 403 1555 1555 2.56 LINK OP1 DC D 3 NA NA A 404 1555 1555 2.64 LINK O HOH D 104 NA NA A 404 1555 1555 2.71 LINK O LYS A 60 NA NA A 404 1555 1555 2.43 LINK O LEU A 62 NA NA A 404 1555 1555 2.34 LINK O VAL A 65 NA NA A 404 1555 1555 2.25 LINK O THR A 101 NA NA A 403 1555 1555 2.25 LINK O VAL A 103 NA NA A 403 1555 1555 2.48 LINK O ILE A 106 NA NA A 403 1555 1555 2.41 LINK OD1 ASP A 190 MG MG A 402 1555 1555 2.01 LINK OD1 ASP A 190 NA NA A 405 1555 1555 3.16 LINK OD2 ASP A 190 NA NA A 405 1555 1555 2.12 LINK OD2 ASP A 192 MG MG A 402 1555 1555 2.03 LINK OD1 ASP A 192 NA NA A 405 1555 1555 2.15 LINK OD2 ASP A 256 NA NA A 405 1555 1555 2.20 LINK O1A H84 A 401 MG MG A 402 1555 1555 2.00 LINK O1G H84 A 401 MG MG A 402 1555 1555 2.20 LINK O1B H84 A 401 MG MG A 402 1555 1555 2.08 LINK O1A H84 A 401 NA NA A 405 1555 1555 2.40 LINK MG MG A 402 O HOH A 554 1555 1555 2.24 LINK NA NA A 403 O HOH A 803 1555 1555 2.59 LINK NA NA A 404 O HOH A 557 1555 1555 2.61 CISPEP 1 GLY A 274 SER A 275 0 0.89 SITE 1 AC1 25 GLY A 179 SER A 180 ARG A 183 SER A 188 SITE 2 AC1 25 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 AC1 25 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 AC1 25 ASN A 279 MG A 402 NA A 405 HOH A 554 SITE 5 AC1 25 HOH A 562 HOH A 673 HOH A 704 HOH A 743 SITE 6 AC1 25 HOH A 766 DOC P 10 HOH P 102 DT T 6 SITE 7 AC1 25 DG T 7 SITE 1 AC2 5 ASP A 190 ASP A 192 H84 A 401 NA A 405 SITE 2 AC2 5 HOH A 554 SITE 1 AC3 6 THR A 101 VAL A 103 ILE A 106 HOH A 803 SITE 2 AC3 6 DG P 9 HOH P 106 SITE 1 AC4 6 LYS A 60 LEU A 62 VAL A 65 HOH A 557 SITE 2 AC4 6 DC D 3 HOH D 104 SITE 1 AC5 7 ASP A 190 ASP A 192 ASP A 256 H84 A 401 SITE 2 AC5 7 MG A 402 DOC P 10 HOH P 102 SITE 1 AC6 3 ALA A 32 HIS A 34 LYS A 35 SITE 1 AC7 2 ASN A 294 THR A 297 CRYST1 50.874 79.669 55.784 90.00 107.72 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 0.019656 0.000000 0.006280 0.00000 SCALE2 0.000000 0.012552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018819 0.00000