HEADER TRANSFERASE/DNA 09-FEB-12 4DO9 TITLE TERNARY COMPLEX OF DNA POLYMERASE BETA WITH A DIDEOXY TERMINATED TITLE 2 PRIMER AND 2'-DEOXYGUANOSINE 5'-BETA, GAMMA-MONOFLUOROMETHYLENE TITLE 3 TRIPHOSPHATE: STEREOSELECTIVE BINDING OF R-ISOMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA POLYMERASE BETA; COMPND 5 EC: 2.7.7.7, 4.2.99.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: C C G A C C G C G C A T C A G C; COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: G C T G A T G C G (DOC); COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: G T C G G; 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 OTHER_DETAILS: CHEMICALLY SYNTHESIZED OLIGONUCLEOTIDE; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: CHEMICALLY SYNTHESIZED OLIGONUCLEOTIDE; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 OTHER_DETAILS: CHEMICALLY SYNTHESIZED OLIGONUCLEOTIDE KEYWDS STEREOSELECTIVITY, DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.K.BATRA REVDAT 2 13-SEP-23 4DO9 1 REMARK LINK REVDAT 1 13-JUN-12 4DO9 0 JRNL AUTH Y.WU,V.M.ZAKHAROVA,B.A.KASHEMIROV,M.F.GOODMAN,V.K.BATRA, JRNL AUTH 2 S.H.WILSON,C.E.MCKENNA JRNL TITL BETA,GAMMA-CHF- AND BETA,GAMMA-CHCL-DGTP DIASTEREOMERS: JRNL TITL 2 SYNTHESIS, DISCRETE (31)P NMR SIGNATURES, AND ABSOLUTE JRNL TITL 3 CONFIGURATIONS OF NEW STEREOCHEMICAL PROBES FOR DNA JRNL TITL 4 POLYMERASES JRNL REF J.AM.CHEM.SOC. V. 134 8734 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22397499 JRNL DOI 10.1021/JA300218X REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.7 REMARK 3 NUMBER OF REFLECTIONS : 23090 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1832 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 20.2829 - 4.7968 0.99 1904 165 0.1704 0.2098 REMARK 3 2 4.7968 - 3.8157 0.96 1818 156 0.1366 0.1825 REMARK 3 3 3.8157 - 3.3358 0.99 1872 162 0.1827 0.2304 REMARK 3 4 3.3358 - 3.0319 0.96 1800 158 0.1955 0.2499 REMARK 3 5 3.0319 - 2.8152 0.83 1554 132 0.2140 0.2859 REMARK 3 6 2.8152 - 2.6496 0.83 1558 135 0.2250 0.2716 REMARK 3 7 2.6496 - 2.5171 0.85 1597 140 0.2244 0.2420 REMARK 3 8 2.5171 - 2.4077 0.85 1590 137 0.2209 0.3088 REMARK 3 9 2.4077 - 2.3152 0.88 1643 143 0.2138 0.3039 REMARK 3 10 2.3152 - 2.2354 0.89 1707 146 0.2082 0.2825 REMARK 3 11 2.2354 - 2.1656 0.90 1674 140 0.2195 0.3350 REMARK 3 12 2.1656 - 2.1037 0.75 1419 122 0.2144 0.2910 REMARK 3 13 2.1037 - 2.0484 0.60 1122 96 0.1990 0.2479 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 37.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.77970 REMARK 3 B22 (A**2) : -0.43330 REMARK 3 B33 (A**2) : -0.34640 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.36690 REMARK 3 B23 (A**2) : 0.00000 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 3423 REMARK 3 ANGLE : 1.126 4748 REMARK 3 CHIRALITY : 0.064 519 REMARK 3 PLANARITY : 0.004 503 REMARK 3 DIHEDRAL : 19.101 1376 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 4DO9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-11 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 : 25195 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.42700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 2PXI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, PH 7.5 350 MM SODIUM REMARK 280 ACETATE 18% PEG3350 , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 39.95700 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: 6860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -122.0 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 GLU A 123 CG CD OE1 OE2 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 P 9 O3' DG P 9 C3' -0.039 REMARK 500 DG D 1 P DG D 1 OP3 -0.122 REMARK 500 REMARK 500 REMARK: NULL 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 DC T 6 O4' - C1' - N1 ANGL. DEV. = -6.6 DEGREES REMARK 500 DT T 12 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG T 15 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC P 2 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DC P 2 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG P 9 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG D 5 O4' - C1' - N9 ANGL. DEV. = 3.2 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 VAL A 29 -60.79 -99.83 REMARK 500 LYS A 60 1.73 -66.22 REMARK 500 ASP A 170 119.76 -163.40 REMARK 500 CYS A 178 -135.15 -111.97 REMARK 500 ASP A 246 -14.08 76.68 REMARK 500 SER A 275 -178.69 -66.30 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 LYS A 60 O REMARK 620 2 LEU A 62 O 100.1 REMARK 620 3 VAL A 65 O 91.9 85.3 REMARK 620 4 HOH A 727 O 87.4 78.4 163.3 REMARK 620 5 DC D 3 OP1 167.0 92.6 86.3 98.0 REMARK 620 6 HOH D 102 O 95.2 163.5 87.9 108.8 71.9 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 THR A 101 O REMARK 620 2 VAL A 103 O 100.6 REMARK 620 3 ILE A 106 O 89.2 85.8 REMARK 620 4 HOH A 548 O 86.7 101.2 172.5 REMARK 620 5 DG P 9 OP1 157.6 100.8 98.6 83.0 REMARK 620 6 HOH P 101 O 71.8 168.9 86.1 86.7 87.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 99.5 REMARK 620 3 GFH A 410 O1G 92.8 166.0 REMARK 620 4 GFH A 410 O1A 99.2 88.4 83.1 REMARK 620 5 GFH A 410 O2B 177.7 82.6 85.2 81.7 REMARK 620 6 HOH A 501 O 87.3 88.9 98.4 173.3 91.9 REMARK 620 N 1 2 3 4 5 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 ASP A 190 OD2 REMARK 620 2 ASP A 192 OD1 109.4 REMARK 620 3 ASP A 256 OD2 120.8 98.9 REMARK 620 4 GFH A 410 O1A 71.7 87.0 162.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG 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 CL 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 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GFH A 410 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PXI RELATED DB: PDB REMARK 900 STEREOSELECTIVE BINDING FROM A DIASTEREOISOMER MIXTURE REMARK 900 RELATED ID: 4DOA RELATED DB: PDB REMARK 900 RELATED ID: 4DOB RELATED DB: PDB REMARK 900 RELATED ID: 4DOC RELATED DB: PDB DBREF 4DO9 A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4DO9 T 1 16 PDB 4DO9 4DO9 1 16 DBREF 4DO9 P 1 10 PDB 4DO9 4DO9 1 10 DBREF 4DO9 D 1 5 PDB 4DO9 4DO9 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 DC 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 MODRES 4DO9 DOC P 10 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC P 10 18 HET MG A 401 1 HET NA A 402 1 HET NA A 403 1 HET NA A 404 1 HET CL A 405 1 HET CL A 406 1 HET CL A 407 1 HET CL A 408 1 HET CL A 409 1 HET GFH A 410 32 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM GFH 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO) HETNAM 2 GFH METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY) HETNAM 3 GFH PHOSPHORYL]GUANOSINE FORMUL 3 DOC C9 H14 N3 O6 P FORMUL 5 MG MG 2+ FORMUL 6 NA 3(NA 1+) FORMUL 9 CL 5(CL 1-) FORMUL 14 GFH C11 H17 F N5 O12 P3 FORMUL 15 HOH *329(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 TYR A 49 1 18 HELIX 3 3 SER A 55 LYS A 60 1 6 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 GLY A 144 LYS A 148 5 5 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 ARG A 258 N 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 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' DG P 9 P DOC P 10 1555 1555 1.60 LINK O LYS A 60 NA NA A 404 1555 1555 2.74 LINK O LEU A 62 NA NA A 404 1555 1555 2.79 LINK O VAL A 65 NA NA A 404 1555 1555 2.66 LINK O THR A 101 NA NA A 403 1555 1555 2.63 LINK O VAL A 103 NA NA A 403 1555 1555 2.71 LINK O ILE A 106 NA NA A 403 1555 1555 2.74 LINK OD1 ASP A 190 MG MG A 401 1555 1555 2.08 LINK OD2 ASP A 190 NA NA A 402 1555 1555 2.76 LINK OD2 ASP A 192 MG MG A 401 1555 1555 2.22 LINK OD1 ASP A 192 NA NA A 402 1555 1555 2.54 LINK OD2 ASP A 256 NA NA A 402 1555 1555 2.79 LINK MG MG A 401 O1G GFH A 410 1555 1555 2.09 LINK MG MG A 401 O1A GFH A 410 1555 1555 2.16 LINK MG MG A 401 O2B GFH A 410 1555 1555 2.19 LINK MG MG A 401 O HOH A 501 1555 1555 2.12 LINK NA NA A 402 O1A GFH A 410 1555 1555 2.98 LINK NA NA A 403 O HOH A 548 1555 1555 3.03 LINK NA NA A 403 OP1 DG P 9 1555 1555 2.53 LINK NA NA A 403 O HOH P 101 1555 1555 2.59 LINK NA NA A 404 O HOH A 727 1555 1555 2.69 LINK NA NA A 404 OP1 DC D 3 1555 1555 2.86 LINK NA NA A 404 O HOH D 102 1555 1555 2.89 CISPEP 1 GLY A 274 SER A 275 0 2.41 SITE 1 AC1 4 ASP A 190 ASP A 192 GFH A 410 HOH A 501 SITE 1 AC2 5 ASP A 190 ASP A 192 ASP A 256 GFH A 410 SITE 2 AC2 5 DOC P 10 SITE 1 AC3 6 THR A 101 VAL A 103 ILE A 106 HOH A 548 SITE 2 AC3 6 DG P 9 HOH P 101 SITE 1 AC4 6 LYS A 60 LEU A 62 VAL A 65 HOH A 727 SITE 2 AC4 6 DC D 3 HOH D 102 SITE 1 AC5 5 GLN A 264 TYR A 266 CYS A 267 VAL A 313 SITE 2 AC5 5 HOH A 509 SITE 1 AC6 4 ALA A 32 ILE A 33 HIS A 34 LYS A 35 SITE 1 AC7 3 LYS A 81 LEU A 82 ARG A 89 SITE 1 AC8 3 ASN A 294 THR A 297 ARG A 299 SITE 1 AC9 3 GLU A 329 PRO A 330 LYS A 331 SITE 1 BC1 25 GLY A 179 SER A 180 ARG A 183 GLY A 189 SITE 2 BC1 25 ASP A 190 ASP A 192 TYR A 271 PHE A 272 SITE 3 BC1 25 THR A 273 GLY A 274 ASP A 276 ASN A 279 SITE 4 BC1 25 ARG A 283 MG A 401 NA A 402 HOH A 501 SITE 5 BC1 25 HOH A 507 HOH A 533 HOH A 611 HOH A 633 SITE 6 BC1 25 HOH A 702 HOH A 740 DOC P 10 DC T 6 SITE 7 BC1 25 DG T 7 CRYST1 50.693 79.914 55.607 90.00 107.66 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 0.019727 0.000000 0.006278 0.00000 SCALE2 0.000000 0.012513 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018872 0.00000