HEADER TRANSFERASE/DNA 29-JUN-04 1TVA TITLE HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A TITLE 2 MISMATCHED TEMPLATE THYMIDINE AND INCOMING CYTIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'; COMPND 3 CHAIN: T; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3'; COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(P*GP*TP*CP*GP*G)-3'; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA POLYMERASE BETA; COMPND 15 CHAIN: A; COMPND 16 EC: 2.7.7.7; COMPND 17 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 GENE: POLB; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOTIDYLTRANSFERASE, DNA REPAIR, DNA MISMATCH, BASE EXCISION KEYWDS 2 REPAIR, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.KRAHN,W.A.BEARD,S.H.WILSON REVDAT 3 14-FEB-24 1TVA 1 REMARK LINK REVDAT 2 24-FEB-09 1TVA 1 VERSN REVDAT 1 23-NOV-04 1TVA 0 JRNL AUTH J.M.KRAHN,W.A.BEARD,S.H.WILSON JRNL TITL STRUCTURAL INSIGHTS INTO DNA POLYMERASE BETA DETERRENTS FOR JRNL TITL 2 MISINCORPORATION SUPPORT AN INDUCED-FIT MECHANISM FOR JRNL TITL 3 FIDELITY JRNL REF STRUCTURE V. 12 1823 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15458631 JRNL DOI 10.1016/J.STR.2004.08.001 REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 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) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 13567 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) : 0.212 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 667 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.69 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4060 REMARK 3 BIN FREE R VALUE : 0.5590 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 64 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.064 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2645 REMARK 3 NUCLEIC ACID ATOMS : 649 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.93500 REMARK 3 B22 (A**2) : -3.13500 REMARK 3 B33 (A**2) : -7.79900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 7.44700 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 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) : 0.38 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) : 1.189 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.77 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.108 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.544 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.598 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.197 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.170 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS REMARK 3 KSOL : 0.43 REMARK 3 BSOL : 62.99 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: CNS BULK SOLVENT MODEL. PARAMETERS FOR REMARK 3 B-FORM SPECIFIC DNA DIHEDRAL RESTRAINTS IN CNS WERE EXCLUDED REMARK 3 BECAUSE MANY OF THE NUCLEIC ACIDS DEVIATE FROM STRICT B-FORM REMARK 3 GEOMETRY. REMARK 4 REMARK 4 1TVA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000022935. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-98 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 : YALE MIRRORS REMARK 200 OPTICS : YALE MIRRORS 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 : 13572 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.26200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 350 MM SODIUM ACETATE, REMARK 280 50MM IMIDAZOLE, 10MM MGCL2, PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 290K 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 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 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 5 CG CD CE NZ REMARK 470 LYS A 209 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 -0.090 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 LEU A 11 -71.88 -53.47 REMARK 500 PRO A 50 32.44 -84.98 REMARK 500 ASP A 170 115.55 -169.76 REMARK 500 CYS A 178 -145.37 -99.16 REMARK 500 SER A 204 -144.88 -109.16 REMARK 500 GLN A 207 100.62 29.93 REMARK 500 LYS A 230 118.25 -163.19 REMARK 500 ASP A 246 -38.28 79.97 REMARK 500 VAL A 303 -48.55 66.90 REMARK 500 GLN A 324 72.83 54.88 REMARK 500 ARG A 333 37.16 -71.83 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 346 O 88.3 REMARK 620 3 HOH P 347 O 85.1 96.2 REMARK 620 4 THR A 101 O 167.8 79.7 93.9 REMARK 620 5 VAL A 103 O 96.7 165.7 97.6 95.5 REMARK 620 6 ILE A 106 O 90.4 80.9 174.7 90.0 85.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG P 343 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 11 OP1 REMARK 620 2 HOH P 353 O 89.2 REMARK 620 3 HOH A 350 O 174.8 90.4 REMARK 620 4 HOH A 351 O 92.5 89.1 92.6 REMARK 620 5 HOH A 352 O 88.1 92.5 86.8 178.3 REMARK 620 6 HOH A 353 O 92.7 175.8 88.2 87.0 91.4 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 348 O 85.3 REMARK 620 3 LYS A 60 O 175.8 90.6 REMARK 620 4 LEU A 62 O 95.7 171.0 88.4 REMARK 620 5 VAL A 65 O 95.5 93.3 83.9 95.5 REMARK 620 6 HOH A 349 O 92.9 92.0 88.0 79.0 170.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 345 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 30 O REMARK 620 2 SER A 171 OG 117.3 REMARK 620 3 HOH A 354 O 157.3 85.3 REMARK 620 4 HOH A 356 O 101.5 83.4 82.0 REMARK 620 5 HOH A 357 O 85.7 116.1 82.1 153.5 REMARK 620 N 1 2 3 4 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 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG P 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 345 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BPZ RELATED DB: PDB REMARK 900 A SIMILAR POLYMERASE BETA COMPLEX CONTAINING A CORRECTLY PAIRED REMARK 900 NUCLEIC ACID PRIMER TERMINUS REMARK 900 RELATED ID: 1TV9 RELATED DB: PDB REMARK 900 HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A REMARK 900 MISMATCHED TEMPLATE ADENINE AND INCOMING CYTIDINE DBREF 1TVA A 1 335 UNP P06746 DPOB_HUMAN 0 334 DBREF 1TVA T 1 16 PDB 1TVA 1TVA 1 16 DBREF 1TVA P 1 11 PDB 1TVA 1TVA 1 11 DBREF 1TVA D 1 5 PDB 1TVA 1TVA 1 5 SEQRES 1 T 16 DC DC DG DA DC DT DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 11 DG DC DT DG DA DT DG DC DG DC DC 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 HET MG P 343 1 HET NA A 341 1 HET NA A 342 1 HET PO4 A 344 5 HET MG A 345 1 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 5 MG 2(MG 2+) FORMUL 6 NA 2(NA 1+) FORMUL 8 PO4 O4 P 3- FORMUL 10 HOH *225(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 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 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 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 PRO A 208 VAL A 221 1 14 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 SER A 229 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 OP1 DG P 9 NA NA A 341 1555 1555 2.37 LINK OP1 DC P 11 MG MG P 343 1555 1555 2.10 LINK MG MG P 343 O HOH P 353 1555 1555 2.09 LINK MG MG P 343 O HOH A 350 1555 1555 2.05 LINK MG MG P 343 O HOH A 351 1555 1555 2.08 LINK MG MG P 343 O HOH A 352 1555 1555 2.10 LINK MG MG P 343 O HOH A 353 1555 1555 2.04 LINK O HOH P 346 NA NA A 341 1555 1555 2.38 LINK O HOH P 347 NA NA A 341 1555 1555 2.47 LINK OP1 DC D 3 NA NA A 342 1555 1555 2.48 LINK O HOH D 348 NA NA A 342 1555 1555 2.37 LINK O SER A 30 MG MG A 345 1555 1555 2.14 LINK O LYS A 60 NA NA A 342 1555 1555 2.44 LINK O LEU A 62 NA NA A 342 1555 1555 2.44 LINK O VAL A 65 NA NA A 342 1555 1555 2.41 LINK O THR A 101 NA NA A 341 1555 1555 2.33 LINK O VAL A 103 NA NA A 341 1555 1555 2.40 LINK O ILE A 106 NA NA A 341 1555 1555 2.44 LINK OG SER A 171 MG MG A 345 1655 1555 2.09 LINK NA NA A 342 O HOH A 349 1555 1555 2.40 LINK MG MG A 345 O HOH A 354 1555 1555 3.11 LINK MG MG A 345 O HOH A 356 1555 1555 2.96 LINK MG MG A 345 O HOH A 357 1555 1555 2.13 CISPEP 1 GLY A 274 SER A 275 0 0.16 SITE 1 AC1 6 THR A 101 VAL A 103 ILE A 106 DG P 9 SITE 2 AC1 6 HOH P 346 HOH P 347 SITE 1 AC2 6 LYS A 60 LEU A 62 VAL A 65 HOH A 349 SITE 2 AC2 6 DC D 3 HOH D 348 SITE 1 AC3 8 ASP A 192 HOH A 350 HOH A 351 HOH A 352 SITE 2 AC3 8 HOH A 353 DC P 10 DC P 11 HOH P 353 SITE 1 AC4 6 SER A 180 SER A 188 GLY A 189 ASP A 190 SITE 2 AC4 6 HOH A 353 HOH A 441 SITE 1 AC5 4 SER A 30 SER A 171 HOH A 356 HOH A 357 CRYST1 54.600 79.700 54.600 90.00 106.40 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 0.018315 0.000000 0.005390 0.00000 SCALE2 0.000000 0.012547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019092 0.00000