HEADER LYASE/DNA 03-MAR-20 6W13 TITLE HUMAN 8-OXOGUANINE GLYCOSYLASE INTERROGATING FULLY INTRAHELICAL OXOG TITLE 2 LESION DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-GLYCOSYLASE/DNA LYASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.-,4.2.99.18; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*CP*AP*(8OG)P*GP*TP*CP*T)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*AP*CP*CP*TP*GP*G)-3'); COMPND 13 CHAIN: C; COMPND 14 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: OGG1, MMH, MUTM, OGH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS HOGG1, 8-OXOG, ENCOUNTER COMPLEX, INTERROGATION COMPLEX, DNA BINDING KEYWDS 2 PROTEIN, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR U.SHIGDEL,G.VERDINE REVDAT 2 18-OCT-23 6W13 1 REMARK REVDAT 1 23-SEP-20 6W13 0 JRNL AUTH U.K.SHIGDEL,V.OVCHINNIKOV,S.J.LEE,J.A.SHIH,M.KARPLUS,K.NAM, JRNL AUTH 2 G.L.VERDINE JRNL TITL THE TRAJECTORY OF INTRAHELICAL LESION RECOGNITION AND JRNL TITL 2 EXTRUSION BY THE HUMAN 8-OXOGUANINE DNA GLYCOSYLASE. JRNL REF NAT COMMUN V. 11 4437 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32895378 JRNL DOI 10.1038/S41467-020-18290-2 REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20290 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 + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1098 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1438 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.3910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2484 REMARK 3 NUCLEIC ACID ATOMS : 267 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.45000 REMARK 3 B33 (A**2) : -1.45000 REMARK 3 B12 (A**2) : 0.22000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.290 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.245 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.207 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.345 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2830 ; 0.008 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2486 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3905 ; 1.361 ; 1.871 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5707 ; 2.590 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 313 ; 5.659 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;32.845 ;23.214 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 378 ;12.912 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.552 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 412 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3042 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 678 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6W13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100.000 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21460 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 45.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.25000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1EBM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE, PH 6.1, 200 REMARK 280 MM MGOAC, AND 17 % POLYETHYLENE GLYCOL 8000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 140.53533 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 70.26767 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 105.40150 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 35.13383 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 175.66917 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 140.53533 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 70.26767 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 35.13383 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 105.40150 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 175.66917 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 557 LIES ON A SPECIAL POSITION. 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 465 GLN A 325 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 30 CZ NH1 NH2 REMARK 480 GLU A 71 CD OE1 OE2 REMARK 480 GLN A 84 CD OE1 NE2 REMARK 480 LYS A 98 CD CE NZ REMARK 480 GLN A 121 OE1 NE2 REMARK 480 GLN A 125 CG CD OE1 NE2 REMARK 480 LYS A 126 CG CD CE NZ REMARK 480 SER A 148 OG REMARK 480 ARG A 154 CD NE CZ NH1 NH2 REMARK 480 ARG A 206 NE CZ NH1 NH2 REMARK 480 LYS A 249 NZ REMARK 480 GLN A 287 CG CD OE1 NE2 REMARK 480 LYS A 289 CD CE NZ REMARK 480 GLN A 294 CD OE1 NE2 REMARK 480 LYS A 297 CE NZ REMARK 480 ARG A 324 CG CD NE CZ NH1 NH2 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 28 104.37 -171.70 REMARK 500 LEU A 33 114.56 -168.31 REMARK 500 GLN A 43 -63.51 -93.58 REMARK 500 THR A 69 -167.54 -105.35 REMARK 500 LEU A 170 -68.52 -96.93 REMARK 500 ASP A 174 -125.55 53.26 REMARK 500 PRO A 309 -18.54 -49.74 REMARK 500 LEU A 323 99.64 -69.56 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 43 O REMARK 620 2 GLN A 135 OE1 69.5 REMARK 620 3 HOH A 555 O 106.1 90.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 175 OD2 REMARK 620 2 TRP A 307 O 17.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 187 O REMARK 620 2 GLY A 189 O 109.1 REMARK 620 3 SER A 209 OG 109.6 135.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 241 O REMARK 620 2 LEU A 243 O 96.0 REMARK 620 3 VAL A 246 O 81.7 86.7 REMARK 620 4 HOH A 536 O 80.9 85.8 160.2 REMARK 620 5 DC B 26 OP2 138.9 123.0 87.5 111.9 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 MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue S5Y B 101 DBREF 6W13 A 12 325 UNP O15527 OGG1_HUMAN 12 325 DBREF 6W13 B 21 27 PDB 6W13 6W13 21 27 DBREF 6W13 C 5 10 PDB 6W13 6W13 5 10 SEQADV 6W13 GLY A 9 UNP O15527 EXPRESSION TAG SEQADV 6W13 SER A 10 UNP O15527 EXPRESSION TAG SEQADV 6W13 GLU A 11 UNP O15527 EXPRESSION TAG SEQADV 6W13 GLN A 122 UNP O15527 GLU 122 ENGINEERED MUTATION SEQADV 6W13 CYS A 207 UNP O15527 TYR 207 ENGINEERED MUTATION SEQADV 6W13 TRP A 253 UNP O15527 CYS 253 ENGINEERED MUTATION 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 GLN 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 CYS 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 LYS VAL ALA ASP TRP 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 SEQRES 1 B 7 DC DA 8OG DG DT DC DT SEQRES 1 C 6 DA DC DC DT DG DG HET 8OG B 23 23 HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HET MG A 404 1 HET ACT A 405 4 HET ACT A 406 4 HET S5Y B 101 16 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM S5Y 2-(2-ETHOXYETHOXY)ETHANETHIOL HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 4 MG 4(MG 2+) FORMUL 8 ACT 2(C2 H3 O2 1-) FORMUL 10 S5Y C6 H14 O2 S FORMUL 11 HOH *85(H2 O) HELIX 1 AA1 THR A 19 TRP A 23 5 5 HELIX 2 AA2 ARG A 34 LEU A 39 1 6 HELIX 3 AA3 THR A 89 GLN A 101 1 13 HELIX 4 AA4 THR A 105 ASP A 117 1 13 HELIX 5 AA5 ASP A 117 GLN A 125 1 9 HELIX 6 AA6 ASP A 136 CYS A 146 1 11 HELIX 7 AA7 ASN A 151 GLY A 167 1 17 HELIX 8 AA8 SER A 183 ALA A 188 1 6 HELIX 9 AA9 GLU A 191 LEU A 199 1 9 HELIX 10 AB1 TYR A 203 GLN A 219 1 17 HELIX 11 AB2 GLY A 221 GLN A 227 1 7 HELIX 12 AB3 SER A 232 ILE A 242 1 11 HELIX 13 AB4 GLY A 247 LEU A 259 1 13 HELIX 14 AB5 ASP A 268 SER A 280 1 13 HELIX 15 AB6 SER A 292 GLY A 308 1 17 HELIX 16 AB7 TYR A 310 LEU A 323 1 14 SHEET 1 AA1 5 ALA A 24 PRO A 27 0 SHEET 2 AA1 5 GLN A 72 TYR A 78 -1 O LEU A 73 N ILE A 26 SHEET 3 AA1 5 GLN A 62 GLN A 68 -1 N THR A 67 O HIS A 74 SHEET 4 AA1 5 HIS A 54 LEU A 59 -1 N TRP A 55 O LEU A 66 SHEET 5 AA1 5 ARG A 48 SER A 51 -1 N ARG A 48 O SER A 56 SHEET 1 AA2 2 ARG A 169 LEU A 173 0 SHEET 2 AA2 2 VAL A 176 HIS A 179 -1 O TYR A 178 N LEU A 170 LINK SG ACYS A 207 S AS5Y B 101 1555 1555 2.05 LINK SG BCYS A 207 S BS5Y B 101 1555 1555 1.93 LINK O3' DA B 22 P 8OG B 23 1555 1555 1.61 LINK O3' 8OG B 23 P DG B 24 1555 1555 1.59 LINK N2 DG B 24 C S5Y B 101 1555 1555 1.46 LINK O GLN A 43 MG MG A 401 1555 1555 2.95 LINK OE1 GLN A 135 MG MG A 401 1555 1555 2.71 LINK OD2 ASP A 175 MG MG A 403 1555 5555 2.65 LINK O LEU A 187 MG MG A 404 1555 1555 2.89 LINK O GLY A 189 MG MG A 404 1555 1555 2.91 LINK OG SER A 209 MG MG A 404 1555 1555 2.30 LINK O CYS A 241 MG MG A 402 1555 1555 2.36 LINK O LEU A 243 MG MG A 402 1555 1555 2.56 LINK O VAL A 246 MG MG A 402 1555 1555 2.58 LINK O TRP A 307 MG MG A 403 1555 1555 2.51 LINK MG MG A 401 O HOH A 555 1555 1555 2.99 LINK MG MG A 402 O HOH A 536 1555 1555 2.55 LINK MG MG A 402 OP2 DC B 26 1555 1555 2.33 SITE 1 AC1 4 GLN A 43 GLN A 135 SER A 143 HOH A 555 SITE 1 AC2 5 CYS A 241 LEU A 243 VAL A 246 HOH A 536 SITE 2 AC2 5 DC B 26 SITE 1 AC3 7 HIS A 112 TRP A 113 ASP A 175 TRP A 307 SITE 2 AC3 7 GLY A 308 PRO A 309 TYR A 310 SITE 1 AC4 6 LEU A 187 ALA A 188 GLY A 189 VAL A 192 SITE 2 AC4 6 SER A 209 ARG A 213 SITE 1 AC5 3 TYR A 233 ASP A 252 HOH A 534 SITE 1 AC6 4 VAL A 58 ASP A 136 GLU A 139 HOH A 501 SITE 1 AC7 5 TYR A 203 CYS A 207 DG B 24 DT B 25 SITE 2 AC7 5 DC C 7 CRYST1 90.707 90.707 210.803 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 0.011025 0.006365 0.000000 0.00000 SCALE2 0.000000 0.012730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004744 0.00000