HEADER TRANSFERASE, LYASE/DNA 15-APR-11 3RJH
TITLE TERNARY COMPLEX OF DNA POLYMERASE BETA WITH A GAPPED DNA CONTAINING
TITLE 2 (SYN)8ODG:DA AT PRIMER TERMINUS AND DG:DCMP(CF2)PPIN THE ACTIVE SITE
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*GP*(8OG)
COMPND 8 P*CP*GP*CP*AP*TP*CP*AP*GP*C)-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*A)-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 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 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES;
SOURCE 15 MOL_ID: 4;
SOURCE 16 SYNTHETIC: YES
KEYWDS MUTAGENESIS, G-T TRANSVERSION, DNA POLYMERASE, OXIDATIVE DAMAGE,
KEYWDS 2 TRANSFERASE, LYASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR V.K.BATRA,W.A.BEARD,S.H.WILSON
REVDAT 2 13-SEP-23 3RJH 1 REMARK LINK
REVDAT 1 18-JAN-12 3RJH 0
JRNL AUTH V.K.BATRA,D.D.SHOCK,W.A.BEARD,C.E.MCKENNA,S.H.WILSON
JRNL TITL BINARY COMPLEX CRYSTAL STRUCTURE OF DNA POLYMERASE BETA
JRNL TITL 2 REVEALS MULTIPLE CONFORMATIONS OF THE TEMPLATING
JRNL TITL 3 8-OXOGUANINE LESION
JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 113 2012
JRNL REFN ISSN 0027-8424
JRNL PMID 22178760
JRNL DOI 10.1073/PNAS.1112235108
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
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) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.35
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 482367.320
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.8
REMARK 3 NUMBER OF REFLECTIONS : 18949
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) : 0.204
REMARK 3 FREE R VALUE : 0.259
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1869
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.90
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2848
REMARK 3 BIN R VALUE (WORKING SET) : 0.2500
REMARK 3 BIN FREE R VALUE : 0.3230
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.00
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 351
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2608
REMARK 3 NUCLEIC ACID ATOMS : 635
REMARK 3 HETEROGEN ATOMS : 38
REMARK 3 SOLVENT ATOMS : 302
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 21.50
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.70
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 4.29000
REMARK 3 B22 (A**2) : -2.42000
REMARK 3 B33 (A**2) : -1.86000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 5.43000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26
REMARK 3 ESD FROM SIGMAA (A) : 0.24
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) : 0.35
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.005
REMARK 3 BOND ANGLES (DEGREES) : 1.100
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.920
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) : 1.330 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.110 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.080 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.030 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.34
REMARK 3 BSOL : 42.69
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 : CTF.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 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 : 8OG.TOP
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3RJH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-11.
REMARK 100 THE DEPOSITION ID IS D_1000065007.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-APR-06
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 : 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 : 18949
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 3.500
REMARK 200 R MERGE (I) : 0.07500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000
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 (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.36100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.210
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 2FMS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.84
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, PH 7.5, 350 MM SODIUM
REMARK 280 ACETATE, 18 % PEG3350, 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 39.95500
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: 6450 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19580 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 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 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 248 CG CD CE NZ
REMARK 470 VAL A 303 CG1 CG2
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 -0.084
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 78.05 -116.85
REMARK 500 ASP A 170 113.71 -167.96
REMARK 500 CYS A 178 -127.09 -112.59
REMARK 500 ASP A 246 -17.47 70.77
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 405 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 60 O
REMARK 620 2 LEU A 62 O 86.0
REMARK 620 3 VAL A 65 O 86.5 85.4
REMARK 620 4 HOH A 595 O 97.4 74.4 159.1
REMARK 620 5 DC D 3 OP1 167.5 92.8 81.0 94.2
REMARK 620 6 HOH D 108 O 101.1 169.2 86.8 112.3 78.5
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 THR A 101 O
REMARK 620 2 VAL A 103 O 92.7
REMARK 620 3 ILE A 106 O 87.4 91.0
REMARK 620 4 HOH A 524 O 66.9 159.6 88.0
REMARK 620 5 HOH A 584 O 79.9 79.7 163.8 96.1
REMARK 620 6 DG P 9 OP1 160.7 102.8 103.5 97.2 91.6
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 101.2
REMARK 620 3 6CF A 401 O1G 86.2 168.7
REMARK 620 4 6CF A 401 O1A 108.6 86.7 99.1
REMARK 620 5 6CF A 401 O2B 160.1 85.7 84.6 90.2
REMARK 620 6 HOH A 503 O 75.8 87.5 86.1 173.4 86.0
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 403 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 190 OD2
REMARK 620 2 ASP A 192 OD1 97.6
REMARK 620 3 ASP A 256 OD2 87.9 89.8
REMARK 620 4 6CF A 401 O1A 98.3 92.4 173.1
REMARK 620 5 HOH A 505 O 88.6 173.1 93.5 83.6
REMARK 620 6 DA P 10 O3' 167.5 90.9 83.0 90.4 83.5
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 6CF 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 MG 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
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 408
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 409
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3RJE RELATED DB: PDB
REMARK 900 RELATED ID: 3RJF RELATED DB: PDB
REMARK 900 RELATED ID: 3RJG RELATED DB: PDB
REMARK 900 RELATED ID: 3RJI RELATED DB: PDB
REMARK 900 RELATED ID: 3RJJ RELATED DB: PDB
REMARK 900 RELATED ID: 3RJK RELATED DB: PDB
DBREF 3RJH A 1 335 UNP P06746 DPOLB_HUMAN 1 335
DBREF 3RJH T 1 16 PDB 3RJH 3RJH 1 16
DBREF 3RJH P 1 10 PDB 3RJH 3RJH 1 10
DBREF 3RJH D 1 5 PDB 3RJH 3RJH 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 DG 8OG 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 DA
SEQRES 1 D 5 DG DT DC DG DG
MODRES 3RJH 8OG T 7 DG
HET 8OG T 7 23
HET 6CF A 401 30
HET MG A 402 1
HET MG A 403 1
HET NA A 404 1
HET NA A 405 1
HET CL A 406 1
HET CL A 407 1
HET CL A 408 1
HET CL A 409 1
HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETNAM 6CF 2'-DEOXY-5'-O-[(S)-{DIFLUORO[(S)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 6CF PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]CYTIDINE
HETNAM MG MAGNESIUM ION
HETNAM NA SODIUM ION
HETNAM CL CHLORIDE ION
HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
FORMUL 2 8OG C10 H14 N5 O8 P
FORMUL 5 6CF C10 H16 F2 N3 O12 P3
FORMUL 6 MG 2(MG 2+)
FORMUL 8 NA 2(NA 1+)
FORMUL 10 CL 4(CL 1-)
FORMUL 14 HOH *302(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 ASP A 116 1 10
HELIX 8 8 THR A 121 LYS A 127 1 7
HELIX 9 9 ASN A 128 LEU A 132 5 5
HELIX 10 10 ASN A 133 TYR A 142 1 10
HELIX 11 11 TYR A 142 LYS A 148 1 7
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 ILE A 174 VAL A 177 0
SHEET 2 B 5 MET A 191 THR A 196 -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 200 THR A 201 0
SHEET 2 C 2 SER A 204 THR A 205 -1 O SER A 204 N THR A 201
SHEET 1 D 2 PHE A 291 ILE A 293 0
SHEET 2 D 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292
LINK O3' DG T 6 P 8OG T 7 1555 1555 1.61
LINK O3' 8OG T 7 P DC T 8 1555 1555 1.61
LINK O LYS A 60 NA NA A 405 1555 1555 2.35
LINK O LEU A 62 NA NA A 405 1555 1555 2.58
LINK O VAL A 65 NA NA A 405 1555 1555 2.68
LINK O THR A 101 NA NA A 404 1555 1555 2.46
LINK O VAL A 103 NA NA A 404 1555 1555 2.52
LINK O ILE A 106 NA NA A 404 1555 1555 2.50
LINK OD1 ASP A 190 MG MG A 402 1555 1555 1.94
LINK OD2 ASP A 190 MG MG A 403 1555 1555 2.00
LINK OD2 ASP A 192 MG MG A 402 1555 1555 2.05
LINK OD1 ASP A 192 MG MG A 403 1555 1555 2.02
LINK OD2 ASP A 256 MG MG A 403 1555 1555 2.02
LINK O1G 6CF A 401 MG MG A 402 1555 1555 1.90
LINK O1A 6CF A 401 MG MG A 402 1555 1555 1.93
LINK O2B 6CF A 401 MG MG A 402 1555 1555 2.00
LINK O1A 6CF A 401 MG MG A 403 1555 1555 2.19
LINK MG MG A 402 O HOH A 503 1555 1555 2.18
LINK MG MG A 403 O HOH A 505 1555 1555 2.24
LINK MG MG A 403 O3' DA P 10 1555 1555 2.22
LINK NA NA A 404 O HOH A 524 1555 1555 2.37
LINK NA NA A 404 O HOH A 584 1555 1555 2.63
LINK NA NA A 404 OP1 DG P 9 1555 1555 2.27
LINK NA NA A 405 O HOH A 595 1555 1555 2.70
LINK NA NA A 405 OP1 DC D 3 1555 1555 2.59
LINK NA NA A 405 O HOH D 108 1555 1555 2.31
CISPEP 1 GLY A 274 SER A 275 0 1.34
SITE 1 AC1 23 GLY A 179 SER A 180 ARG A 183 SER A 188
SITE 2 AC1 23 GLY A 189 ASP A 190 ASP A 192 TYR A 271
SITE 3 AC1 23 PHE A 272 THR A 273 GLY A 274 ASP A 276
SITE 4 AC1 23 ASN A 279 MG A 402 MG A 403 HOH A 503
SITE 5 AC1 23 HOH A 504 HOH A 505 HOH A 515 HOH A 645
SITE 6 AC1 23 HOH A 655 DA P 10 DG T 6
SITE 1 AC2 5 ASP A 190 ASP A 192 6CF A 401 MG A 403
SITE 2 AC2 5 HOH A 503
SITE 1 AC3 7 ASP A 190 ASP A 192 ASP A 256 6CF A 401
SITE 2 AC3 7 MG A 402 HOH A 505 DA P 10
SITE 1 AC4 6 THR A 101 VAL A 103 ILE A 106 HOH A 524
SITE 2 AC4 6 HOH A 584 DG P 9
SITE 1 AC5 6 LYS A 60 LEU A 62 VAL A 65 HOH A 595
SITE 2 AC5 6 DC D 3 HOH D 108
SITE 1 AC6 3 ASN A 294 THR A 297 ARG A 299
SITE 1 AC7 3 GLN A 264 TYR A 266 CYS A 267
SITE 1 AC8 4 ALA A 32 ILE A 33 HIS A 34 LYS A 35
SITE 1 AC9 4 LYS A 81 LEU A 82 ARG A 89 HOH A 717
CRYST1 50.530 79.910 55.460 90.00 108.04 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 0.019790 0.000000 0.006446 0.00000
SCALE2 0.000000 0.012514 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018963 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
