HEADER TRANSFERASE/DNA 13-SEP-02 1MQ3 TITLE HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA CONTAINING AN 8- TITLE 2 OXO-7,8-DIHYDRO-GUANINE TEMPLATE PAIRED WITH DCTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*AP*CP*(8OG)P*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: 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: 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; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, DNA, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.KRAHN,W.A.BEARD,H.MILLER,A.P.GROLLMAN,S.H.WILSON REVDAT 4 14-FEB-24 1MQ3 1 REMARK LINK REVDAT 3 24-FEB-09 1MQ3 1 VERSN REVDAT 2 08-APR-03 1MQ3 1 JRNL REMARK REVDAT 1 28-JAN-03 1MQ3 0 JRNL AUTH J.M.KRAHN,W.A.BEARD,H.MILLER,A.P.GROLLMAN,S.H.WILSON JRNL TITL STRUCTURE OF DNA POLYMERASE BETA WITH THE MUTAGENIC DNA JRNL TITL 2 LESION 8-OXODEOXYGUANINE REVEALS STRUCTURAL INSIGHTS INTO JRNL TITL 3 ITS CODING POTENTIAL JRNL REF STRUCTURE V. 11 121 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12517346 JRNL DOI 10.1016/S0969-2126(02)00930-9 REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 10177 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) : 0.235 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 481 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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 : 2613 REMARK 3 NUCLEIC ACID ATOMS : 632 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -14.23500 REMARK 3 B22 (A**2) : 18.54900 REMARK 3 B33 (A**2) : -4.31300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -15.80600 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL 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) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.324 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.855 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.186 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.869 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 10.00 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 : PROTEIN.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT PARAMETERS FOR 8-OXO-G ARE REMARK 3 BASED ON SEVERAL SMALL MOLECULE OBSERVATIONS. DIHEDRAL REMARK 3 RESTRAINTS FROM DNA-RNA.PARAM WERE DISABLED TO ALLOW FOR REMARK 3 DEVIATIONS FROM CANONICAL B-FORM VALUES, WHICH HAVE BEEN REMARK 3 OBSERVED IN HIGH-RESOLUTION DATA FROM SIMILAR POLYMERASE BETA REMARK 3 DNA COMPLEXES. REMARK 4 REMARK 4 1MQ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017088. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 200.0 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 RU300 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10209 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 2.510 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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: 1BPY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 3350, 350 MM SODIUM ACETATE REMARK 280 AND 50 MM IMIDAZOLE AT 18 DEGREES (C), PH 7.5, TEMPERATURE 291.0K 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 39.95000 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 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 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 VAL A 29 -71.62 -76.31 REMARK 500 PRO A 50 31.12 -80.24 REMARK 500 SER A 55 146.59 -176.49 REMARK 500 ASP A 91 102.31 -49.20 REMARK 500 PHE A 146 -2.09 -57.00 REMARK 500 CYS A 178 -129.06 -82.49 REMARK 500 SER A 202 7.63 -58.71 REMARK 500 GLU A 203 0.40 -159.87 REMARK 500 LYS A 209 40.91 -96.46 REMARK 500 LEU A 228 -91.62 -69.69 REMARK 500 LYS A 230 106.32 -160.17 REMARK 500 LYS A 244 -143.63 -82.33 REMARK 500 ASP A 246 -13.51 66.62 REMARK 500 PHE A 272 -6.51 -57.41 REMARK 500 LEU A 301 56.24 -94.01 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 341 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 HOH P 344 O 84.4 REMARK 620 3 THR A 101 O 166.3 82.0 REMARK 620 4 VAL A 103 O 86.4 163.6 107.3 REMARK 620 5 ILE A 106 O 84.7 77.6 94.2 88.1 REMARK 620 6 HOH A 345 O 99.2 104.1 82.5 90.7 175.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 342 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC D 3 OP1 REMARK 620 2 HOH D 346 O 85.6 REMARK 620 3 LYS A 60 O 174.9 94.8 REMARK 620 4 LEU A 62 O 98.9 170.6 81.4 REMARK 620 5 VAL A 65 O 99.9 91.2 75.0 96.1 REMARK 620 6 HOH A 347 O 91.1 92.8 94.0 78.9 168.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 339 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 89.6 REMARK 620 3 DCP A 338 O1A 81.9 90.7 REMARK 620 4 DCP A 338 O2B 173.5 94.5 93.0 REMARK 620 5 DCP A 338 O3A 123.6 114.5 49.9 50.0 REMARK 620 6 DCP A 338 O1G 93.2 174.6 94.2 83.1 67.5 REMARK 620 7 HOH A 346 O 90.9 91.3 172.5 94.1 134.9 84.1 REMARK 620 N 1 2 3 4 5 6 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 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP A 338 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BPX RELATED DB: PDB REMARK 900 1BPX IS HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA REMARK 900 RELATED ID: 1BPY RELATED DB: PDB REMARK 900 1BPY IS HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND REMARK 900 DDCTP REMARK 900 RELATED ID: 1MQ2 RELATED DB: PDB REMARK 900 1MQ2 IS HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA REMARK 900 CONTAINING AN 8-OXO-7,8-DIHYDRO-GUANINE AND DAMP DBREF 1MQ3 A 1 335 UNP P06746 DPOB_HUMAN 1 335 DBREF 1MQ3 T 1 16 PDB 1MQ3 1MQ3 1 16 DBREF 1MQ3 P 1 10 PDB 1MQ3 1MQ3 1 10 DBREF 1MQ3 D 1 5 PDB 1MQ3 1MQ3 1 5 SEQRES 1 T 16 DC DC DG DA DC 8OG 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 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 MODRES 1MQ3 8OG T 6 DG MODRES 1MQ3 DOC P 10 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET 8OG T 6 23 HET DOC P 10 18 HET MG A 339 1 HET NA A 341 1 HET NA A 342 1 HET DCP A 338 28 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 1 8OG C10 H14 N5 O8 P FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 5 MG MG 2+ FORMUL 6 NA 2(NA 1+) FORMUL 8 DCP C9 H16 N3 O13 P3 FORMUL 9 HOH *78(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 61 1 7 HELIX 4 4 THR A 67 GLY A 80 1 14 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 THR A 93 THR A 101 1 9 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 ASN A 133 PHE A 143 1 11 HELIX 10 10 GLY A 144 LYS A 148 5 5 HELIX 11 11 ARG A 152 ASP A 170 1 19 HELIX 12 12 CYS A 178 ARG A 183 1 6 HELIX 13 13 LYS A 209 VAL A 221 1 13 HELIX 14 14 PRO A 261 ASP A 263 5 3 HELIX 15 15 GLN A 264 GLY A 274 1 11 HELIX 16 16 SER A 275 GLY A 290 1 16 HELIX 17 17 SER A 315 ILE A 323 1 9 HELIX 18 18 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 ASP A 226 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 O3' DC T 5 P 8OG T 6 1555 1555 1.61 LINK O3' 8OG T 6 P DG T 7 1555 1555 1.61 LINK O3' DG P 9 P DOC P 10 1555 1555 1.61 LINK OP1 DG P 9 NA NA A 341 1555 1555 2.25 LINK O HOH P 344 NA NA A 341 1555 1555 2.25 LINK OP1 DC D 3 NA NA A 342 1555 1555 2.50 LINK O HOH D 346 NA NA A 342 1555 1555 2.43 LINK O LYS A 60 NA NA A 342 1555 1555 2.39 LINK O LEU A 62 NA NA A 342 1555 1555 2.49 LINK O VAL A 65 NA NA A 342 1555 1555 2.52 LINK O THR A 101 NA NA A 341 1555 1555 2.25 LINK O VAL A 103 NA NA A 341 1555 1555 2.45 LINK O ILE A 106 NA NA A 341 1555 1555 2.59 LINK OD1 ASP A 190 MG MG A 339 1555 1555 1.83 LINK OD2 ASP A 192 MG MG A 339 1555 1555 2.11 LINK O1A DCP A 338 MG MG A 339 1555 1555 1.98 LINK O2B DCP A 338 MG MG A 339 1555 1555 1.94 LINK O3A DCP A 338 MG MG A 339 1555 1555 3.14 LINK O1G DCP A 338 MG MG A 339 1555 1555 2.09 LINK MG MG A 339 O HOH A 346 1555 1555 1.98 LINK NA NA A 341 O HOH A 345 1555 1555 2.60 LINK NA NA A 342 O HOH A 347 1555 1555 2.55 CISPEP 1 GLY A 274 SER A 275 0 0.52 SITE 1 AC1 4 ASP A 190 ASP A 192 DCP A 338 HOH A 346 SITE 1 AC2 6 THR A 101 VAL A 103 ILE A 106 HOH A 345 SITE 2 AC2 6 DG P 9 HOH P 344 SITE 1 AC3 6 LYS A 60 LEU A 62 VAL A 65 HOH A 347 SITE 2 AC3 6 DC D 3 HOH D 346 SITE 1 AC4 20 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC4 20 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 AC4 20 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 AC4 20 ASN A 279 MG A 339 HOH A 346 HOH A 354 SITE 5 AC4 20 HOH A 389 DOC P 10 8OG T 6 DG T 7 CRYST1 50.500 79.900 55.600 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 0.012516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018901 0.00000