HEADER TRANSFERASE/DNA 24-FEB-09 3GDX
TITLE DNA POLYMERASE BETA WITH A GAPPED DND SUBSTRATE AND DTMP(CF2)PP
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(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3';
COMPND 8 CHAIN: T;
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(P*GP*TP*CP*GP*G)-3';
COMPND 16 CHAIN: D;
COMPND 17 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 MOL_ID: 3;
SOURCE 11 SYNTHETIC: YES;
SOURCE 12 MOL_ID: 4;
SOURCE 13 SYNTHETIC: YES
KEYWDS NUCLOETIDYL TRANSFERASE, DNA POLYMERASE, DNA DAMAGE, DNA REPAIR, DNA
KEYWDS 2 REPLICATION, DNA SYNTHESIS, DNA-BINDING, DNA-DIRECTED DNA
KEYWDS 3 POLYMERASE, LYASE, MAGNESIUM, METAL-BINDING, NUCLEOTIDYLTRANSFERASE,
KEYWDS 4 NUCLEUS, POLYMORPHISM, SODIUM, TRANSFERASE, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.H.WILSON,V.K.BATRA,L.C.PEDERSEN
REVDAT 2 06-SEP-23 3GDX 1 REMARK LINK
REVDAT 1 05-MAY-09 3GDX 0
JRNL AUTH T.G.UPTON,B.A.KASHEMIROV,C.E.MCKENNA,M.F.GOODMAN,
JRNL AUTH 2 G.K.PRAKASH,R.KULTYSHEV,V.K.BATRA,D.D.SHOCK,L.C.PEDERSEN,
JRNL AUTH 3 W.A.BEARD,S.H.WILSON
JRNL TITL ALPHA,BETA-DIFLUOROMETHYLENE DEOXYNUCLEOSIDE
JRNL TITL 2 5'-TRIPHOSPHATES: A CONVENIENT SYNTHESIS OF USEFUL PROBES
JRNL TITL 3 FOR DNA POLYMERASE BETA STRUCTURE AND FUNCTION
JRNL REF ORG.LETT. V. 11 1883 2009
JRNL REFN ISSN 1523-7060
JRNL PMID 19351147
JRNL DOI 10.1021/OL701755K
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) : 20.58
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 333638.110
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 74.9
REMARK 3 NUMBER OF REFLECTIONS : 15889
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) : 0.208
REMARK 3 FREE R VALUE : 0.266
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800
REMARK 3 FREE R VALUE TEST SET COUNT : 1559
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007
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) (%) : 75.30
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2359
REMARK 3 BIN R VALUE (WORKING SET) : 0.2810
REMARK 3 BIN FREE R VALUE : 0.3450
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 271
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2609
REMARK 3 NUCLEIC ACID ATOMS : 631
REMARK 3 HETEROGEN ATOMS : 37
REMARK 3 SOLVENT ATOMS : 277
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 17.50
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.80
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.09000
REMARK 3 B22 (A**2) : -1.14000
REMARK 3 B33 (A**2) : -0.94000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 5.36000
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) : 0.29
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) : 0.37
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.38
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) : 24.00
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.010
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) : 2.140 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.920 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.890 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.32
REMARK 3 BSOL : 34.13
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 : 4BD.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 : DTF.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 3GDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-09.
REMARK 100 THE DEPOSITION ID IS D_1000051739.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-APR-05
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) : 1.5418
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 : 18597
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 (%) : 86.4
REMARK 200 DATA REDUNDANCY : 2.300
REMARK 200 R MERGE (I) : 0.09800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000
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 (%) : 82.2
REMARK 200 DATA REDUNDANCY IN SHELL : 2.50
REMARK 200 R MERGE FOR SHELL (I) : 0.43800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.280
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 (%): 44.20
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM IMIDAZOLE,PH 8.0, SODIUM
REMARK 280 ACETATE 350 MM, PEG2000 MONOMETHYL ETHER 20%, 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 39.85000
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: 6090 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19900 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 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 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 74.89 -115.78
REMARK 500 ASP A 170 118.04 -172.73
REMARK 500 CYS A 178 -129.17 -110.41
REMARK 500 ASP A 190 -169.35 -162.65
REMARK 500 THR A 205 68.34 -117.66
REMARK 500 LYS A 206 4.43 -55.00
REMARK 500 LYS A 209 13.68 55.88
REMARK 500 ASP A 246 -22.23 71.00
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 MG A 347 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 1 O
REMARK 620 2 ASP A 190 OD1 84.1
REMARK 620 3 ASP A 192 OD2 86.5 108.1
REMARK 620 4 4BD A 346 O1A 162.6 112.9 84.5
REMARK 620 5 4BD A 346 O2B 78.8 160.8 79.7 85.0
REMARK 620 6 4BD A 346 O3G 91.2 87.2 164.2 93.5 84.5
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 348 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 2 O
REMARK 620 2 ASP A 190 OD2 81.3
REMARK 620 3 ASP A 192 OD1 165.8 88.8
REMARK 620 4 ASP A 256 OD2 93.0 92.9 97.5
REMARK 620 5 4BD A 346 O1A 78.5 92.0 91.9 169.5
REMARK 620 6 DC P 10 O3' 89.9 169.2 101.0 81.4 92.3
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 350 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 60 O
REMARK 620 2 LEU A 62 O 82.1
REMARK 620 3 VAL A 65 O 87.7 90.4
REMARK 620 4 DC D 3 OP1 172.3 96.9 84.7
REMARK 620 5 HOH D 55 O 93.0 169.4 80.1 86.8
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 349 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 THR A 101 O
REMARK 620 2 VAL A 103 O 93.2
REMARK 620 3 ILE A 106 O 97.4 88.8
REMARK 620 4 HOH A 510 O 79.9 86.1 174.1
REMARK 620 5 DG P 9 OP1 165.6 93.4 95.5 87.8
REMARK 620 6 HOH P 56 O 76.3 166.9 100.2 84.4 95.2
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 4BD A 346
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 347
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 348
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 349
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 350
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 351
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 352
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2FMS RELATED DB: PDB
DBREF 3GDX A 10 335 UNP P06746 DPOLB_HUMAN 10 335
DBREF 3GDX T 1 16 PDB 3GDX 3GDX 1 16
DBREF 3GDX P 1 10 PDB 3GDX 3GDX 1 10
DBREF 3GDX D 1 5 PDB 3GDX 3GDX 1 5
SEQRES 1 A 326 THR LEU ASN GLY GLY ILE THR ASP MET LEU THR GLU LEU
SEQRES 2 A 326 ALA ASN PHE GLU LYS ASN VAL SER GLN ALA ILE HIS LYS
SEQRES 3 A 326 TYR ASN ALA TYR ARG LYS ALA ALA SER VAL ILE ALA LYS
SEQRES 4 A 326 TYR PRO HIS LYS ILE LYS SER GLY ALA GLU ALA LYS LYS
SEQRES 5 A 326 LEU PRO GLY VAL GLY THR LYS ILE ALA GLU LYS ILE ASP
SEQRES 6 A 326 GLU PHE LEU ALA THR GLY LYS LEU ARG LYS LEU GLU LYS
SEQRES 7 A 326 ILE ARG GLN ASP ASP THR SER SER SER ILE ASN PHE LEU
SEQRES 8 A 326 THR ARG VAL SER GLY ILE GLY PRO SER ALA ALA ARG LYS
SEQRES 9 A 326 PHE VAL ASP GLU GLY ILE LYS THR LEU GLU ASP LEU ARG
SEQRES 10 A 326 LYS ASN GLU ASP LYS LEU ASN HIS HIS GLN ARG ILE GLY
SEQRES 11 A 326 LEU LYS TYR PHE GLY ASP PHE GLU LYS ARG ILE PRO ARG
SEQRES 12 A 326 GLU GLU MET LEU GLN MET GLN ASP ILE VAL LEU ASN GLU
SEQRES 13 A 326 VAL LYS LYS VAL ASP SER GLU TYR ILE ALA THR VAL CYS
SEQRES 14 A 326 GLY SER PHE ARG ARG GLY ALA GLU SER SER GLY ASP MET
SEQRES 15 A 326 ASP VAL LEU LEU THR HIS PRO SER PHE THR SER GLU SER
SEQRES 16 A 326 THR LYS GLN PRO LYS LEU LEU HIS GLN VAL VAL GLU GLN
SEQRES 17 A 326 LEU GLN LYS VAL HIS PHE ILE THR ASP THR LEU SER LYS
SEQRES 18 A 326 GLY GLU THR LYS PHE MET GLY VAL CYS GLN LEU PRO SER
SEQRES 19 A 326 LYS ASN ASP GLU LYS GLU TYR PRO HIS ARG ARG ILE ASP
SEQRES 20 A 326 ILE ARG LEU ILE PRO LYS ASP GLN TYR TYR CYS GLY VAL
SEQRES 21 A 326 LEU TYR PHE THR GLY SER ASP ILE PHE ASN LYS ASN MET
SEQRES 22 A 326 ARG ALA HIS ALA LEU GLU LYS GLY PHE THR ILE ASN GLU
SEQRES 23 A 326 TYR THR ILE ARG PRO LEU GLY VAL THR GLY VAL ALA GLY
SEQRES 24 A 326 GLU PRO LEU PRO VAL ASP SER GLU LYS ASP ILE PHE ASP
SEQRES 25 A 326 TYR ILE GLN TRP LYS TYR ARG GLU PRO LYS ASP ARG SER
SEQRES 26 A 326 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 4BD A 346 31
HET MG A 347 1
HET MG A 348 1
HET NA A 349 1
HET NA A 350 1
HET CL A 351 1
HET CL A 352 1
HETNAM 4BD 5'-O-[(S)-{DIFLUORO[(S)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 4BD PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]THYMIDINE
HETNAM MG MAGNESIUM ION
HETNAM NA SODIUM ION
HETNAM CL CHLORIDE ION
FORMUL 5 4BD C11 H17 F2 N2 O13 P3
FORMUL 6 MG 2(MG 2+)
FORMUL 8 NA 2(NA 1+)
FORMUL 10 CL 2(CL 1-)
FORMUL 12 HOH *277(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 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 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 N ARG A 258 O LEU A 195
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 THR A 225 O VAL A 238
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 O HOH A 1 MG MG A 347 1555 1555 2.21
LINK O HOH A 2 MG MG A 348 1555 1555 2.19
LINK O LYS A 60 NA NA A 350 1555 1555 2.44
LINK O LEU A 62 NA NA A 350 1555 1555 2.45
LINK O VAL A 65 NA NA A 350 1555 1555 2.67
LINK O THR A 101 NA NA A 349 1555 1555 2.26
LINK O VAL A 103 NA NA A 349 1555 1555 2.69
LINK O ILE A 106 NA NA A 349 1555 1555 2.19
LINK OD1 ASP A 190 MG MG A 347 1555 1555 1.80
LINK OD2 ASP A 190 MG MG A 348 1555 1555 2.27
LINK OD2 ASP A 192 MG MG A 347 1555 1555 2.11
LINK OD1 ASP A 192 MG MG A 348 1555 1555 2.02
LINK OD2 ASP A 256 MG MG A 348 1555 1555 2.03
LINK O1A 4BD A 346 MG MG A 347 1555 1555 2.00
LINK O2B 4BD A 346 MG MG A 347 1555 1555 2.20
LINK O3G 4BD A 346 MG MG A 347 1555 1555 2.11
LINK O1A 4BD A 346 MG MG A 348 1555 1555 2.27
LINK MG MG A 348 O3' DC P 10 1555 1555 2.15
LINK NA NA A 349 O HOH A 510 1555 1555 2.73
LINK NA NA A 349 OP1 DG P 9 1555 1555 2.38
LINK NA NA A 349 O HOH P 56 1555 1555 2.22
LINK NA NA A 350 OP1 DC D 3 1555 1555 2.51
LINK NA NA A 350 O HOH D 55 1555 1555 2.64
CISPEP 1 GLY A 274 SER A 275 0 1.64
SITE 1 AC1 23 HOH A 1 HOH A 2 GLY A 179 SER A 180
SITE 2 AC1 23 ARG A 183 GLY A 189 ASP A 190 ASP A 192
SITE 3 AC1 23 TYR A 271 PHE A 272 THR A 273 GLY A 274
SITE 4 AC1 23 ASP A 276 ASN A 279 MG A 347 MG A 348
SITE 5 AC1 23 HOH A 362 HOH A 427 HOH A 448 HOH A 459
SITE 6 AC1 23 HOH A 488 DC P 10 DA T 6
SITE 1 AC2 5 HOH A 1 ASP A 190 ASP A 192 4BD A 346
SITE 2 AC2 5 MG A 348
SITE 1 AC3 7 HOH A 2 ASP A 190 ASP A 192 ASP A 256
SITE 2 AC3 7 4BD A 346 MG A 347 DC P 10
SITE 1 AC4 6 THR A 101 VAL A 103 ILE A 106 HOH A 510
SITE 2 AC4 6 DG P 9 HOH P 56
SITE 1 AC5 5 LYS A 60 LEU A 62 VAL A 65 DC D 3
SITE 2 AC5 5 HOH D 55
SITE 1 AC6 3 ASN A 294 THR A 297 ARG A 299
SITE 1 AC7 4 GLN A 264 CYS A 267 VAL A 313 HOH A 450
CRYST1 50.500 79.700 55.300 90.00 107.90 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 0.019802 0.000000 0.006396 0.00000
SCALE2 0.000000 0.012547 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019003 0.00000