HEADER LYASE/DNA 24-JAN-00 1EBM TITLE CRYSTAL STRUCTURE OF THE HUMAN 8-OXOGUANINE GLYCOSYLASE (HOGG1) BOUND TITLE 2 TO A SUBSTRATE OLIGONUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(8OG) COMPND 3 P*GP*TP*CP*TP*AP*CP*C)-3'); COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)- COMPND 8 3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 8-OXOGUANINE DNA GLYCOSYLASE; COMPND 13 CHAIN: A; COMPND 14 FRAGMENT: CORE FRAGMENT (RESIDUES 12 TO 325); COMPND 15 SYNONYM: AP LYASE; COMPND 16 ENGINEERED: YES; COMPND 17 MUTATION: 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 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET30A-HOGG1 KEYWDS DNA REPAIR, DNA GLYCOSYLASE, PROTEIN/DNA, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.D.BRUNER,D.P.NORMAN,G.L.VERDINE REVDAT 3 07-FEB-24 1EBM 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1EBM 1 VERSN REVDAT 1 20-MAR-00 1EBM 0 JRNL AUTH S.D.BRUNER,D.P.NORMAN,G.L.VERDINE JRNL TITL STRUCTURAL BASIS FOR RECOGNITION AND REPAIR OF THE JRNL TITL 2 ENDOGENOUS MUTAGEN 8-OXOGUANINE IN DNA. JRNL REF NATURE V. 403 859 2000 JRNL REFN ISSN 0028-0836 JRNL PMID 10706276 JRNL DOI 10.1038/35002510 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3795094.090 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 29194 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) : 0.232 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2938 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3707 REMARK 3 BIN R VALUE (WORKING SET) : 0.3190 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 429 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2439 REMARK 3 NUCLEIC ACID ATOMS : 610 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.76000 REMARK 3 B22 (A**2) : 2.76000 REMARK 3 B33 (A**2) : -5.52000 REMARK 3 B12 (A**2) : 2.58000 REMARK 3 B13 (A**2) : 0.00000 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) : 0.30 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) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.950 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) : 1.140 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.860 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.530 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.360 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 51.32 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_REP.PA REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PA REMARK 3 PARAMETER FILE 3 : WATER_REP.PARA REMARK 3 PARAMETER FILE 4 : ION.PARAM 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 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EBM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000010437. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9350 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29194 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.38400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, SODIUM CACODYLATE, CALCIUM REMARK 280 ACETATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 141.91467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 70.95733 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 106.43600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.47867 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 177.39333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 141.91467 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 70.95733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 35.47867 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 106.43600 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 177.39333 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A PROTEIN MONOMER BOUND TO A REMARK 300 DUPLEX DNA 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 GLY A 80 REMARK 465 ASP A 81 REMARK 465 LYS A 82 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 71 CG CD OE1 OE2 REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 ARG A 87 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 122 CG CD OE1 OE2 REMARK 470 GLN A 125 CG CD OE1 NE2 REMARK 470 GLN A 128 CG CD OE1 NE2 REMARK 470 ARG A 134 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 164 CG CD OE1 NE2 REMARK 470 GLN A 227 CG CD OE1 NE2 REMARK 470 SER A 286 OG REMARK 470 LYS A 289 CG CD CE NZ REMARK 470 GLN A 294 CG CD OE1 NE2 REMARK 470 GLN A 325 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 429 O HOH A 430 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 424 O HOH A 424 10665 1.20 REMARK 500 O3' DC D 16 O3' DC D 16 11655 2.04 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 CYS A 28 106.42 -171.19 REMARK 500 GLN A 43 -60.80 -95.29 REMARK 500 THR A 69 -159.17 -108.95 REMARK 500 LEU A 170 -99.25 -97.30 REMARK 500 ASP A 174 -125.56 60.12 REMARK 500 LYS A 261 78.35 -110.92 REMARK 500 ASP A 268 -167.11 -115.67 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 CA C 17 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA C 24 OP2 REMARK 620 2 HOH C 63 O 97.6 REMARK 620 3 HOH C 86 O 163.4 89.8 REMARK 620 4 HOH C 146 O 88.5 101.6 104.7 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 CA C 17 DBREF 1EBM A 9 325 UNP O15527 OGG1_HUMAN 12 325 DBREF 1EBM C 18 32 PDB 1EBM 1EBM 18 32 DBREF 1EBM D 2 16 PDB 1EBM 1EBM 2 16 SEQADV 1EBM GLY A 9 UNP O15527 ARG 12 CONFLICT SEQADV 1EBM SER A 10 UNP O15527 ARG 13 CONFLICT SEQADV 1EBM GLU A 11 UNP O15527 MET 14 CONFLICT SEQADV 1EBM GLN A 249 UNP O15527 LYS 252 CONFLICT SEQRES 1 C 15 DG DC DG DT DC DC DA 8OG DG DT DC DT DA SEQRES 2 C 15 DC DC SEQRES 1 D 15 DG DG DT DA DG DA DC DC DT DG DG DA DC SEQRES 2 D 15 DG DC SEQRES 1 A 317 GLY SER GLU GLY HIS ARG THR LEU ALA SER THR PRO ALA SEQRES 2 A 317 LEU TRP ALA SER ILE PRO CYS PRO ARG SER GLU LEU ARG SEQRES 3 A 317 LEU ASP LEU VAL LEU PRO SER GLY GLN SER PHE ARG TRP SEQRES 4 A 317 ARG GLU GLN SER PRO ALA HIS TRP SER GLY VAL LEU ALA SEQRES 5 A 317 ASP GLN VAL TRP THR LEU THR GLN THR GLU GLU GLN LEU SEQRES 6 A 317 HIS CYS THR VAL TYR ARG GLY ASP LYS SER GLN ALA SER SEQRES 7 A 317 ARG PRO THR PRO ASP GLU LEU GLU ALA VAL ARG LYS TYR SEQRES 8 A 317 PHE GLN LEU ASP VAL THR LEU ALA GLN LEU TYR HIS HIS SEQRES 9 A 317 TRP GLY SER VAL ASP SER HIS PHE GLN GLU VAL ALA GLN SEQRES 10 A 317 LYS PHE GLN GLY VAL ARG LEU LEU ARG GLN ASP PRO ILE SEQRES 11 A 317 GLU CYS LEU PHE SER PHE ILE CYS SER SER ASN ASN ASN SEQRES 12 A 317 ILE ALA ARG ILE THR GLY MET VAL GLU ARG LEU CYS GLN SEQRES 13 A 317 ALA PHE GLY PRO ARG LEU ILE GLN LEU ASP ASP VAL THR SEQRES 14 A 317 TYR HIS GLY PHE PRO SER LEU GLN ALA LEU ALA GLY PRO SEQRES 15 A 317 GLU VAL GLU ALA HIS LEU ARG LYS LEU GLY LEU GLY TYR SEQRES 16 A 317 ARG ALA ARG TYR VAL SER ALA SER ALA ARG ALA ILE LEU SEQRES 17 A 317 GLU GLU GLN GLY GLY LEU ALA TRP LEU GLN GLN LEU ARG SEQRES 18 A 317 GLU SER SER TYR GLU GLU ALA HIS LYS ALA LEU CYS ILE SEQRES 19 A 317 LEU PRO GLY VAL GLY THR GLN VAL ALA ASP CYS ILE CYS SEQRES 20 A 317 LEU MET ALA LEU ASP LYS PRO GLN ALA VAL PRO VAL ASP SEQRES 21 A 317 VAL HIS MET TRP HIS ILE ALA GLN ARG ASP TYR SER TRP SEQRES 22 A 317 HIS PRO THR THR SER GLN ALA LYS GLY PRO SER PRO GLN SEQRES 23 A 317 THR ASN LYS GLU LEU GLY ASN PHE PHE ARG SER LEU TRP SEQRES 24 A 317 GLY PRO TYR ALA GLY TRP ALA GLN ALA VAL LEU PHE SER SEQRES 25 A 317 ALA ASP LEU ARG GLN MODRES 1EBM 8OG C 25 DG HET 8OG C 25 23 HET CA C 17 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 1 8OG C10 H14 N5 O8 P FORMUL 4 CA CA 2+ FORMUL 5 HOH *133(H2 O) HELIX 1 1 THR A 19 TRP A 23 5 5 HELIX 2 2 ARG A 34 LEU A 39 1 6 HELIX 3 3 THR A 89 PHE A 100 1 12 HELIX 4 4 THR A 105 ASP A 117 1 13 HELIX 5 5 ASP A 117 GLN A 125 1 9 HELIX 6 6 ASP A 136 CYS A 146 1 11 HELIX 7 7 ASN A 151 GLY A 167 1 17 HELIX 8 8 SER A 183 ALA A 188 1 6 HELIX 9 9 GLU A 191 LEU A 199 1 9 HELIX 10 10 TYR A 203 GLU A 218 1 16 HELIX 11 11 GLY A 220 LEU A 228 1 9 HELIX 12 12 SER A 232 CYS A 241 1 10 HELIX 13 13 GLY A 247 LEU A 259 1 13 HELIX 14 14 ASP A 268 SER A 280 1 13 HELIX 15 15 SER A 292 GLY A 308 1 17 HELIX 16 16 TYR A 310 ARG A 324 1 15 SHEET 1 A 5 ALA A 24 PRO A 27 0 SHEET 2 A 5 GLN A 72 TYR A 78 -1 N LEU A 73 O ILE A 26 SHEET 3 A 5 VAL A 63 GLN A 68 -1 O VAL A 63 N TYR A 78 SHEET 4 A 5 HIS A 54 VAL A 58 -1 N TRP A 55 O LEU A 66 SHEET 5 A 5 ARG A 48 SER A 51 -1 O ARG A 48 N SER A 56 SHEET 1 B 2 ARG A 169 LEU A 173 0 SHEET 2 B 2 VAL A 176 HIS A 179 -1 O VAL A 176 N LEU A 173 LINK O3' DA C 24 P 8OG C 25 1555 1555 1.60 LINK O3' 8OG C 25 P DG C 26 1555 1555 1.60 LINK CA CA C 17 OP2 DA C 24 1555 1555 3.09 LINK CA CA C 17 O HOH C 63 1555 1555 2.65 LINK CA CA C 17 O HOH C 86 1555 1555 2.29 LINK CA CA C 17 O HOH C 146 1555 1555 2.48 SITE 1 AC1 4 DA C 24 HOH C 63 HOH C 86 HOH C 146 CRYST1 92.357 92.357 212.872 90.00 90.00 120.00 P 65 2 2 12 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 0.010828 0.006251 0.000000 0.00000 SCALE2 0.000000 0.012503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004698 0.00000