HEADER TRANSFERASE/DNA 25-AUG-09 3ISD
TITLE TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH AN ABASIC SITE
TITLE 2 (THF): DAPCPP MISMATCH
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: 5'-D(P*GP*TP*CP*GP*G)-3';
COMPND 8 CHAIN: D;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 3;
COMPND 11 MOLECULE: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3';
COMPND 12 CHAIN: P;
COMPND 13 ENGINEERED: YES;
COMPND 14 MOL_ID: 4;
COMPND 15 MOLECULE: 5'-D(*CP*CP*GP*AP*CP*(3DR)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-
COMPND 16 3';
COMPND 17 CHAIN: T;
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 EXPRESSION_SYSTEM_STRAIN: TAP56;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PWL11;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 14 ORGANISM_TAXID: 32630;
SOURCE 15 OTHER_DETAILS: CHEMICALLY SYTNTHESIZED OLIGONUCLEOTIDE;
SOURCE 16 MOL_ID: 3;
SOURCE 17 SYNTHETIC: YES;
SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 19 ORGANISM_TAXID: 32630;
SOURCE 20 OTHER_DETAILS: CHEMICALLY SYTNTHESIZED OLIGONUCLEOTIDE;
SOURCE 21 MOL_ID: 4;
SOURCE 22 SYNTHETIC: YES;
SOURCE 23 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 24 ORGANISM_TAXID: 32630;
SOURCE 25 OTHER_DETAILS: CHEMICALLY SYTNTHESIZED OLIGONUCLEOTIDE
KEYWDS NUCLEOTIDYL TRANSFERASE, DNA POLYMERASE BETA, ABASIC SITE,
KEYWDS 2 TETRAHYDROFURAN, TERNARY COMPLEX, GAPPED DNA, 'A-RULE', DNA DAMAGE,
KEYWDS 3 DNA REPAIR, DNA REPLICATION, DNA SYNTHESIS, DNA-BINDING, DNA-
KEYWDS 4 DIRECTED DNA POLYMERASE, LYASE, MAGNESIUM, METAL-BINDING,
KEYWDS 5 METHYLATION, NUCLEOTIDYLTRANSFERASE, NUCLEUS, POLYMORPHISM, SODIUM,
KEYWDS 6 TRANSFERASE, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR W.A.BEARD,D.D.SHOCK,V.K.BATRA,L.C.PEDERSEN,S.H.WILSON
REVDAT 5 06-SEP-23 3ISD 1 REMARK LINK
REVDAT 4 06-FEB-19 3ISD 1 COMPND SOURCE REMARK DBREF
REVDAT 4 2 1 SEQADV HET HETNAM FORMUL
REVDAT 3 24-NOV-09 3ISD 1 JRNL
REVDAT 2 22-SEP-09 3ISD 1 REMARK
REVDAT 1 15-SEP-09 3ISD 0
JRNL AUTH W.A.BEARD,D.D.SHOCK,V.K.BATRA,L.C.PEDERSEN,S.H.WILSON
JRNL TITL DNA POLYMERASE BETA SUBSTRATE SPECIFICITY: SIDE CHAIN
JRNL TITL 2 MODULATION OF THE "A-RULE".
JRNL REF J.BIOL.CHEM. V. 284 31680 2009
JRNL REFN ISSN 0021-9258
JRNL PMID 19759017
JRNL DOI 10.1074/JBC.M109.029843
REMARK 2
REMARK 2 RESOLUTION. 2.60 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.19
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 533497.790
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.9
REMARK 3 NUMBER OF REFLECTIONS : 12173
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.195
REMARK 3 FREE R VALUE : 0.262
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1092
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2599
REMARK 3 NUCLEIC ACID ATOMS : 621
REMARK 3 HETEROGEN ATOMS : 45
REMARK 3 SOLVENT ATOMS : 268
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 31.10
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.80
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.70000
REMARK 3 B22 (A**2) : -0.88000
REMARK 3 B33 (A**2) : 0.18000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 5.76000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27
REMARK 3 ESD FROM SIGMAA (A) : 0.27
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.42
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.49
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.006
REMARK 3 BOND ANGLES (DEGREES) : 1.100
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.970
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.340 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.270 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.960 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.080 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.33
REMARK 3 BSOL : 42.61
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : F2A.PARAM
REMARK 3 PARAMETER FILE 2 : NULL
REMARK 3 PARAMETER FILE 3 : NULL
REMARK 3 PARAMETER FILE 4 : NULL
REMARK 3 PARAMETER FILE 5 : NULL
REMARK 3 PARAMETER FILE 6 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
REMARK 3 TOPOLOGY FILE 4 : F2A.TOP
REMARK 3 TOPOLOGY FILE 5 : DNTP.TOP
REMARK 3 TOPOLOGY FILE 6 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3ISD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-09.
REMARK 100 THE DEPOSITION ID IS D_1000054805.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-MAY-07
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
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) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : VIRAMAX
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 : 21464
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 200 DATA REDUNDANCY : 3.500
REMARK 200 R MERGE (I) : 0.07800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3
REMARK 200 DATA REDUNDANCY IN SHELL : 3.30
REMARK 200 R MERGE FOR SHELL (I) : 0.33000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: PDB ENTRY 3C2M
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.53
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE PH 7.5, 350 MM SODIUM
REMARK 280 ACETATE, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 38.82000
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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS THE MONOMERIC COMPLEX
REMARK 300 REPRESENTED BY THE ENTIRE CONTENTS OF THE ASYMMETRIC UNIT. THE
REMARK 300 SOFTWARE-GENERATED WORD 'TETRAMERIC' IN REMARK 350 IS A POLYMERIC
REMARK 300 COUNT.
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: 3960 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20310 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.5 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, P, T
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 1
REMARK 465 SER A 2
REMARK 465 LYS A 3
REMARK 465 ARG A 4
REMARK 465 LYS A 5
REMARK 465 ALA A 6
REMARK 465 PRO A 7
REMARK 465 GLN A 8
REMARK 465 GLU A 9
REMARK 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 GLU A 203 CG CD OE1 OE2
REMARK 470 LYS A 244 CG CD CE NZ
REMARK 470 ASP A 246 CG OD1 OD2
REMARK 470 LYS A 248 CG CD CE NZ
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 DG D 1 P DG D 1 OP3 -0.086
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 ALA A 32 77.24 -111.69
REMARK 500 CYS A 178 -145.59 -108.23
REMARK 500 GLU A 203 -103.75 -118.58
REMARK 500 SER A 204 -1.21 53.43
REMARK 500 LYS A 206 147.99 60.87
REMARK 500 LYS A 244 -87.18 -14.37
REMARK 500 ASN A 245 12.60 178.23
REMARK 500 ASP A 246 -43.74 175.22
REMARK 500 GLU A 247 -179.16 -55.44
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 403 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 60 O
REMARK 620 2 LEU A 62 O 105.6
REMARK 620 3 VAL A 65 O 75.2 84.4
REMARK 620 4 DC D 3 OP1 139.1 97.6 74.1
REMARK 620 5 HOH D 6 O 76.2 156.2 73.0 69.4
REMARK 620 N 1 2 3 4
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 THR A 101 O
REMARK 620 2 VAL A 103 O 94.8
REMARK 620 3 ILE A 106 O 97.9 80.8
REMARK 620 4 HOH A 377 O 83.9 90.1 170.8
REMARK 620 5 DG P 9 OP1 178.5 86.1 81.0 97.4
REMARK 620 6 HOH P 36 O 88.4 165.1 84.3 104.8 90.3
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 404 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 190 OD1
REMARK 620 2 ASP A 192 OD2 84.6
REMARK 620 3 F2A A 412 O1A 97.5 92.1
REMARK 620 4 F2A A 412 O2B 165.6 101.7 95.2
REMARK 620 5 F2A A 412 O3G 94.6 177.9 89.9 78.6
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 405 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 190 OD2
REMARK 620 2 ASP A 192 OD1 100.4
REMARK 620 3 ASP A 256 OD2 96.6 96.7
REMARK 620 4 F2A A 412 O1A 76.7 95.4 167.1
REMARK 620 5 DC P 10 O3' 149.6 107.0 93.3 87.5
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN T 406 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH D 10 O
REMARK 620 2 HOH T 144 O 87.8
REMARK 620 3 HOH T 147 O 161.6 109.6
REMARK 620 4 HOH T 150 O 79.9 167.0 83.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA P 401 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DG P 4 N7
REMARK 620 2 HOH P 56 O 91.4
REMARK 620 3 HOH P 184 O 105.6 107.6
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 407
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 408
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 409
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 410
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 411
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F2A A 412
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 413
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA P 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN T 406
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1BPX RELATED DB: PDB
REMARK 900 DNA POLYMERASE BETA/DNA COMPLEX
REMARK 900 RELATED ID: 3C2M RELATED DB: PDB
REMARK 900 TERNARY COMPLEX OF DNA POLYMERASE BETA WITH A G:DAPCPP MISMATCH IN
REMARK 900 THE ACTIVE SITE
REMARK 900 RELATED ID: 3ISB RELATED DB: PDB
REMARK 900 BINARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH A GAPPED DNA,
REMARK 900 HIGHER RESOLUTION STRUCTURE THAN 1BPX
REMARK 900 RELATED ID: 3ISC RELATED DB: PDB
REMARK 900 BINARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH AN ABASIC SITE
REMARK 900 (THF) IN THE GAPPED DNA
DBREF 3ISD A 1 335 UNP P06746 DPOLB_HUMAN 1 335
DBREF 3ISD D 1 5 PDB 3ISD 3ISD 1 5
DBREF 3ISD P 1 10 PDB 3ISD 3ISD 1 10
DBREF 3ISD T 1 16 PDB 3ISD 3ISD 1 16
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 D 5 DG DT DC DG DG
SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DC
SEQRES 1 T 16 DC DC DG DA DC 3DR DG DC DG DC DA DT DC
SEQRES 2 T 16 DA DG DC
HET 3DR T 6 11
HET NA A 402 1
HET NA A 403 1
HET MN A 404 1
HET MN A 405 1
HET MN A 407 1
HET MN A 408 1
HET MN A 409 1
HET MN A 410 1
HET MN A 411 1
HET F2A A 412 30
HET EDO A 413 4
HET NA P 401 1
HET MN T 406 1
HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
HETNAM NA SODIUM ION
HETNAM MN MANGANESE (II) ION
HETNAM F2A 2'-DEOXY-5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 F2A PHOSPHORYL]METHYL}PHOSPHORYL]ADENOSINE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN 3DR ABASIC DIDEOXYRIBOSE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 4 3DR C5 H11 O6 P
FORMUL 5 NA 3(NA 1+)
FORMUL 7 MN 8(MN 2+)
FORMUL 14 F2A C11 H18 N5 O11 P3
FORMUL 15 EDO C2 H6 O2
FORMUL 18 HOH *268(H2 O)
HELIX 1 1 ASN A 12 VAL A 29 1 18
HELIX 2 2 ALA A 32 LYS A 48 1 17
HELIX 3 3 SER A 55 LYS A 61 1 7
HELIX 4 4 GLY A 66 GLY A 80 1 15
HELIX 5 5 LEU A 82 ASP A 91 1 10
HELIX 6 6 ASP A 91 THR A 101 1 11
HELIX 7 7 GLY A 107 GLU A 117 1 11
HELIX 8 8 THR A 121 ASN A 128 1 8
HELIX 9 9 GLU A 129 LEU A 132 5 4
HELIX 10 10 ASN A 133 TYR A 142 1 10
HELIX 11 11 TYR A 142 GLU A 147 1 6
HELIX 12 12 ARG A 152 ASP A 170 1 19
HELIX 13 13 CYS A 178 ARG A 183 1 6
HELIX 14 14 LYS A 209 VAL A 221 1 13
HELIX 15 15 PRO A 261 ASP A 263 5 3
HELIX 16 16 GLN A 264 GLY A 274 1 11
HELIX 17 17 SER A 275 LYS A 289 1 15
HELIX 18 18 SER A 315 ILE A 323 1 9
HELIX 19 19 GLU A 329 ARG A 333 5 5
SHEET 1 A 2 ILE A 150 PRO A 151 0
SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150
SHEET 1 B 5 THR A 176 VAL A 177 0
SHEET 2 B 5 MET A 191 LEU A 195 -1 O LEU A 194 N THR A 176
SHEET 3 B 5 ARG A 253 LEU A 259 1 O ASP A 256 N VAL A 193
SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253
SHEET 5 B 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236
SHEET 1 C 2 PHE A 291 ILE A 293 0
SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292
LINK O3' DC T 5 P 3DR T 6 1555 1555 1.61
LINK O3' 3DR T 6 P DG T 7 1555 1555 1.61
LINK O LYS A 60 NA NA A 403 1555 1555 2.43
LINK O LEU A 62 NA NA A 403 1555 1555 2.03
LINK O VAL A 65 NA NA A 403 1555 1555 2.95
LINK O THR A 101 NA NA A 402 1555 1555 2.12
LINK O VAL A 103 NA NA A 402 1555 1555 2.57
LINK O ILE A 106 NA NA A 402 1555 1555 2.55
LINK OD1 ASP A 190 MN MN A 404 1555 1555 2.14
LINK OD2 ASP A 190 MN MN A 405 1555 1555 2.40
LINK OD2 ASP A 192 MN MN A 404 1555 1555 1.98
LINK OD1 ASP A 192 MN MN A 405 1555 1555 2.06
LINK OD2 ASP A 256 MN MN A 405 1555 1555 2.46
LINK O HOH A 377 NA NA A 402 1555 1555 2.57
LINK NA NA A 402 OP1 DG P 9 1555 1555 2.64
LINK NA NA A 402 O HOH P 36 1555 1555 2.62
LINK NA NA A 403 OP1 DC D 3 1555 1555 2.60
LINK NA NA A 403 O HOH D 6 1555 1555 2.73
LINK MN MN A 404 O1A F2A A 412 1555 1555 2.25
LINK MN MN A 404 O2B F2A A 412 1555 1555 2.14
LINK MN MN A 404 O3G F2A A 412 1555 1555 2.36
LINK MN MN A 405 O1A F2A A 412 1555 1555 2.37
LINK MN MN A 405 O3' DC P 10 1555 1555 2.30
LINK MN MN A 407 O2 EDO A 413 1555 1555 2.14
LINK MN MN A 411 O HOH A 487 1555 1555 2.34
LINK O HOH D 10 MN MN T 406 1555 1555 2.09
LINK N7 DG P 4 NA NA P 401 1555 1555 2.88
LINK O HOH P 56 NA NA P 401 1555 1555 2.89
LINK O HOH P 184 NA NA P 401 1555 1555 2.47
LINK O HOH T 144 MN MN T 406 1555 1555 2.39
LINK O HOH T 147 MN MN T 406 1555 1555 2.26
LINK O HOH T 150 MN MN T 406 1555 1555 2.42
CISPEP 1 GLY A 274 SER A 275 0 0.19
SITE 1 AC1 6 THR A 101 VAL A 103 ILE A 106 HOH A 377
SITE 2 AC1 6 DG P 9 HOH P 36
SITE 1 AC2 7 LYS A 60 LYS A 61 LEU A 62 PRO A 63
SITE 2 AC2 7 VAL A 65 DC D 3 HOH D 6
SITE 1 AC3 5 ASP A 190 ASP A 192 MN A 405 F2A A 412
SITE 2 AC3 5 HOH A 442
SITE 1 AC4 6 ASP A 190 ASP A 192 ASP A 256 MN A 404
SITE 2 AC4 6 F2A A 412 DC P 10
SITE 1 AC5 3 ASP A 124 EDO A 413 HOH A 449
SITE 1 AC6 2 HIS A 285 GLU A 288
SITE 1 AC7 2 HIS A 51 HOH A 516
SITE 1 AC8 2 GLU A 249 HIS A 252
SITE 1 AC9 2 HIS A 222 HOH A 487
SITE 1 BC1 18 GLY A 179 SER A 180 ARG A 183 SER A 188
SITE 2 BC1 18 GLY A 189 ASP A 190 ASP A 192 TYR A 271
SITE 3 BC1 18 PHE A 272 THR A 273 GLY A 274 ASP A 276
SITE 4 BC1 18 ASN A 279 LYS A 280 HOH A 362 MN A 404
SITE 5 BC1 18 MN A 405 DC P 10
SITE 1 BC2 4 ASP A 124 ASP A 314 MN A 407 HOH A 449
SITE 1 BC3 3 DG P 4 HOH P 56 HOH P 184
SITE 1 BC4 5 HOH D 10 DG T 3 HOH T 144 HOH T 147
SITE 2 BC4 5 HOH T 150
CRYST1 54.700 77.640 55.220 90.00 113.67 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 0.018282 0.000000 0.008014 0.00000
SCALE2 0.000000 0.012880 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019773 0.00000