HEADER DNA BINDING PROTEIN 09-MAR-22 7Z5R TITLE STRUCTURE OF THE MOUSE 8-OXOGUANINE DNA GLYCOSYLASE MOGG1 IN COMPLEX TITLE 2 WITH LIGAND TH012035 COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-GLYCOSYLASE/DNA LYASE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 3.2.2.-,4.2.99.18; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: OGG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OGG1, GLYCOSYLASE, INHIBITOR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.R.DAVIES,E.SCALETTI,P.STENMARK REVDAT 2 07-FEB-24 7Z5R 1 REMARK REVDAT 1 22-MAR-23 7Z5R 0 JRNL AUTH J.R.DAVIES,E.SCALETTI,P.STENMARK JRNL TITL STRUCTURE OF THE MOUSE 8-OXOGUANINE DNA GLYCOSYLASE MOGG1 IN JRNL TITL 2 COMPLEX WITH LIGAND TH012035 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 37989 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) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1960 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2745 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.3760 REMARK 3 BIN FREE R VALUE SET COUNT : 166 REMARK 3 BIN FREE R VALUE : 0.4240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7067 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.96000 REMARK 3 B22 (A**2) : -1.63000 REMARK 3 B33 (A**2) : 0.67000 REMARK 3 B12 (A**2) : 0.00000 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): 0.541 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.326 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.298 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.937 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7334 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6701 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10024 ; 1.242 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15254 ; 0.925 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 910 ; 6.277 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 317 ;32.772 ;22.555 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1026 ;15.818 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 53 ;18.784 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1092 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8420 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1839 ; 0.001 ; 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): 3673 ; 3.652 ; 7.201 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3672 ; 3.653 ; 7.201 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4572 ; 5.878 ;10.777 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4573 ; 5.878 ;10.778 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3661 ; 3.171 ; 7.168 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3662 ; 3.170 ; 7.168 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5447 ; 5.248 ;10.705 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8070 ; 8.407 ;56.387 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8062 ; 8.406 ;56.403 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 : MASK 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 REMARK 4 REMARK 4 7Z5R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1292121630. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40059 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 170.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 6G3Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.12 M ALCOHOLS, 0.1M BUFFER SYSTEM 1 REMARK 280 PH 6.5, 30.0 % V/V GOL_P4K, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 40.72950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.07250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.76650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.07250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.72950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.76650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 8 REMARK 465 SER A 9 REMARK 465 GLY A 80 REMARK 465 ASP A 81 REMARK 465 ASP A 82 REMARK 465 SER A 286 REMARK 465 GLN A 287 REMARK 465 ALA A 288 REMARK 465 LYS A 289 REMARK 465 GLN A 325 REMARK 465 GLY B 80 REMARK 465 ASP B 81 REMARK 465 GLY B 189 REMARK 465 PRO B 190 REMARK 465 GLY B 245 REMARK 465 VAL B 246 REMARK 465 SER B 286 REMARK 465 GLN B 287 REMARK 465 ALA B 288 REMARK 465 LYS B 289 REMARK 465 ARG B 324 REMARK 465 GLN B 325 REMARK 465 GLY C 8 REMARK 465 SER C 9 REMARK 465 GLY C 80 REMARK 465 ASP C 81 REMARK 465 ASP C 82 REMARK 465 SER C 286 REMARK 465 GLN C 287 REMARK 465 ALA C 288 REMARK 465 LYS C 289 REMARK 465 ARG C 324 REMARK 465 GLN C 325 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 ASP A 71 CG OD1 OD2 REMARK 470 SER A 83 OG REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 SER B 19 OG REMARK 470 ASP B 61 CG OD1 OD2 REMARK 470 GLU B 70 CG CD OE1 OE2 REMARK 470 ASP B 71 CG OD1 OD2 REMARK 470 ASP B 82 CG OD1 OD2 REMARK 470 GLN B 84 CG CD OE1 NE2 REMARK 470 LEU B 90 CG CD1 CD2 REMARK 470 GLU B 91 CG CD OE1 OE2 REMARK 470 GLU B 94 CG CD OE1 OE2 REMARK 470 LYS B 98 CG CD CE NZ REMARK 470 SER B 115 OG REMARK 470 ARG B 122 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 125 CG CD OE1 NE2 REMARK 470 LYS B 126 CG CD CE NZ REMARK 470 LEU B 141 CG CD1 CD2 REMARK 470 SER B 147 OG REMARK 470 SER B 148 OG REMARK 470 ASN B 149 CG OD1 ND2 REMARK 470 ASN B 150 CG OD1 ND2 REMARK 470 ARG B 154 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 155 CG1 CG2 CD1 REMARK 470 MET B 158 CG SD CE REMARK 470 LEU B 184 CG CD1 CD2 REMARK 470 GLU B 191 CG CD OE1 OE2 REMARK 470 GLU B 193 CG CD OE1 OE2 REMARK 470 HIS B 195 CG ND1 CD2 CE1 NE2 REMARK 470 LEU B 196 CG CD1 CD2 REMARK 470 LYS B 198 CG CD CE NZ REMARK 470 LEU B 201 CG CD1 CD2 REMARK 470 TYR B 203 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 204 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 206 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 209 CG CD NE CZ NH1 NH2 REMARK 470 SER B 211 OG REMARK 470 ILE B 215 CG1 CG2 CD1 REMARK 470 LEU B 216 CG CD1 CD2 REMARK 470 GLU B 217 CG CD OE1 OE2 REMARK 470 GLU B 218 CG CD OE1 OE2 REMARK 470 GLN B 227 CG CD OE1 NE2 REMARK 470 ARG B 229 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 235 CG CD OE1 OE2 REMARK 470 LYS B 238 CG CD CE NZ REMARK 470 LEU B 240 CG CD1 CD2 REMARK 470 THR B 242 OG1 CG2 REMARK 470 LEU B 243 CG CD1 CD2 REMARK 470 CYS B 255 SG REMARK 470 ASP B 260 CG OD1 OD2 REMARK 470 LYS B 284 CG CD CE NZ REMARK 470 SER B 292 OG REMARK 470 LEU B 294 CG CD1 CD2 REMARK 470 LYS B 297 CG CD CE NZ REMARK 470 SER B 320 OG REMARK 470 LEU B 323 CG CD1 CD2 REMARK 470 SER C 17 OG REMARK 470 SER C 18 OG REMARK 470 SER C 19 OG REMARK 470 SER C 51 OG REMARK 470 ASP C 61 CG OD1 OD2 REMARK 470 GLU C 70 CG CD OE1 OE2 REMARK 470 ASP C 71 CG OD1 OD2 REMARK 470 SER C 83 OG REMARK 470 GLN C 84 CG CD OE1 NE2 REMARK 470 VAL C 85 CG1 CG2 REMARK 470 GLU C 94 CG CD OE1 OE2 REMARK 470 ARG C 122 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 125 CG CD OE1 NE2 REMARK 470 LYS C 126 CG CD CE NZ REMARK 470 ASP C 175 CG OD1 OD2 REMARK 470 LYS C 198 CG CD CE NZ REMARK 470 LEU C 199 CG CD1 CD2 REMARK 470 ARG C 206 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 213 CG CD CE NZ REMARK 470 GLU C 217 CG CD OE1 OE2 REMARK 470 GLU C 218 CG CD OE1 OE2 REMARK 470 GLN C 226 CG CD OE1 NE2 REMARK 470 GLN C 227 CG CD OE1 NE2 REMARK 470 GLU C 234 CG CD OE1 OE2 REMARK 470 GLU C 235 CG CD OE1 OE2 REMARK 470 LYS C 284 CG CD CE NZ 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 LYS A 284 CG CD CE NZ 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 28 107.22 -166.71 REMARK 500 LEU A 33 119.58 -166.97 REMARK 500 GLN A 43 -66.31 -107.60 REMARK 500 PHE A 127 65.25 -112.23 REMARK 500 ASP A 174 -126.17 51.86 REMARK 500 ASP A 175 41.11 -105.46 REMARK 500 CYS B 28 114.13 -169.61 REMARK 500 LEU B 33 117.54 -173.65 REMARK 500 GLN B 43 -79.96 -80.72 REMARK 500 SER B 83 -165.21 -162.57 REMARK 500 SER B 148 105.52 -49.93 REMARK 500 ASP B 174 -122.53 48.66 REMARK 500 LEU B 199 -113.16 -72.99 REMARK 500 ASP B 322 -69.52 -105.49 REMARK 500 CYS C 28 108.88 -161.46 REMARK 500 LEU C 33 122.44 -171.40 REMARK 500 ALA C 60 63.45 16.00 REMARK 500 THR C 69 -72.17 -106.10 REMARK 500 GLU C 70 -56.38 -170.89 REMARK 500 VAL C 85 75.80 -67.20 REMARK 500 GLN C 101 51.93 39.92 REMARK 500 ASP C 174 -133.52 51.03 REMARK 500 GLU C 217 -71.59 -74.04 REMARK 500 ALA C 258 -28.59 -154.32 REMARK 500 PRO C 291 64.16 -11.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 568 DISTANCE = 6.05 ANGSTROMS 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 NI A 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 276 NE2 REMARK 620 2 HIS A 282 NE2 93.8 REMARK 620 3 HIS B 276 NE2 88.0 176.0 REMARK 620 4 HIS B 282 NE2 91.4 90.6 93.0 REMARK 620 5 HIS C 276 NE2 87.6 88.8 87.7 178.8 REMARK 620 6 HIS C 282 NE2 172.6 93.5 84.8 87.3 93.8 REMARK 620 N 1 2 3 4 5 DBREF 7Z5R A 9 325 UNP O08760 OGG1_MOUSE 9 325 DBREF 7Z5R B 9 325 UNP O08760 OGG1_MOUSE 9 325 DBREF 7Z5R C 9 325 UNP O08760 OGG1_MOUSE 9 325 SEQADV 7Z5R GLY A 8 UNP O08760 EXPRESSION TAG SEQADV 7Z5R HIS A 10 UNP O08760 SER 10 CONFLICT SEQADV 7Z5R GLY B 8 UNP O08760 EXPRESSION TAG SEQADV 7Z5R HIS B 10 UNP O08760 SER 10 CONFLICT SEQADV 7Z5R GLY C 8 UNP O08760 EXPRESSION TAG SEQADV 7Z5R HIS C 10 UNP O08760 SER 10 CONFLICT SEQRES 1 A 318 GLY SER HIS MET ARG HIS ARG THR LEU SER SER SER PRO SEQRES 2 A 318 ALA LEU TRP ALA SER ILE PRO CYS PRO ARG SER GLU LEU SEQRES 3 A 318 ARG LEU ASP LEU VAL LEU ALA SER GLY GLN SER PHE ARG SEQRES 4 A 318 TRP LYS GLU GLN SER PRO ALA HIS TRP SER GLY VAL LEU SEQRES 5 A 318 ALA ASP GLN VAL TRP THR LEU THR GLN THR GLU ASP GLN SEQRES 6 A 318 LEU TYR CYS THR VAL TYR ARG GLY ASP ASP SER GLN VAL SEQRES 7 A 318 SER ARG PRO THR LEU GLU GLU LEU GLU THR LEU HIS LYS SEQRES 8 A 318 TYR PHE GLN LEU ASP VAL SER LEU ALA GLN LEU TYR SER SEQRES 9 A 318 HIS TRP ALA SER VAL ASP SER HIS PHE GLN ARG VAL ALA SEQRES 10 A 318 GLN LYS PHE GLN GLY VAL ARG LEU LEU ARG GLN ASP PRO SEQRES 11 A 318 THR GLU CYS LEU PHE SER PHE ILE CYS SER SER ASN ASN SEQRES 12 A 318 ASN ILE ALA ARG ILE THR GLY MET VAL GLU ARG LEU CYS SEQRES 13 A 318 GLN ALA PHE GLY PRO ARG LEU ILE GLN LEU ASP ASP VAL SEQRES 14 A 318 THR TYR HIS GLY PHE PRO ASN LEU HIS ALA LEU ALA GLY SEQRES 15 A 318 PRO GLU ALA GLU THR HIS LEU ARG LYS LEU GLY LEU GLY SEQRES 16 A 318 TYR ARG ALA ARG TYR VAL ARG ALA SER ALA LYS ALA ILE SEQRES 17 A 318 LEU GLU GLU GLN GLY GLY PRO ALA TRP LEU GLN GLN LEU SEQRES 18 A 318 ARG VAL ALA PRO TYR GLU GLU ALA HIS LYS ALA LEU CYS SEQRES 19 A 318 THR LEU PRO GLY VAL GLY ALA LYS VAL ALA ASP CYS ILE SEQRES 20 A 318 CYS LEU MET ALA LEU ASP LYS PRO GLN ALA VAL PRO VAL SEQRES 21 A 318 ASP VAL HIS VAL TRP GLN ILE ALA HIS ARG ASP TYR GLY SEQRES 22 A 318 TRP HIS PRO LYS THR SER GLN ALA LYS GLY PRO SER PRO SEQRES 23 A 318 LEU ALA ASN LYS GLU LEU GLY ASN PHE PHE ARG ASN LEU SEQRES 24 A 318 TRP GLY PRO TYR ALA GLY TRP ALA GLN ALA VAL LEU PHE SEQRES 25 A 318 SER ALA ASP LEU ARG GLN SEQRES 1 B 318 GLY SER HIS MET ARG HIS ARG THR LEU SER SER SER PRO SEQRES 2 B 318 ALA LEU TRP ALA SER ILE PRO CYS PRO ARG SER GLU LEU SEQRES 3 B 318 ARG LEU ASP LEU VAL LEU ALA SER GLY GLN SER PHE ARG SEQRES 4 B 318 TRP LYS GLU GLN SER PRO ALA HIS TRP SER GLY VAL LEU SEQRES 5 B 318 ALA ASP GLN VAL TRP THR LEU THR GLN THR GLU ASP GLN SEQRES 6 B 318 LEU TYR CYS THR VAL TYR ARG GLY ASP ASP SER GLN VAL SEQRES 7 B 318 SER ARG PRO THR LEU GLU GLU LEU GLU THR LEU HIS LYS SEQRES 8 B 318 TYR PHE GLN LEU ASP VAL SER LEU ALA GLN LEU TYR SER SEQRES 9 B 318 HIS TRP ALA SER VAL ASP SER HIS PHE GLN ARG VAL ALA SEQRES 10 B 318 GLN LYS PHE GLN GLY VAL ARG LEU LEU ARG GLN ASP PRO SEQRES 11 B 318 THR GLU CYS LEU PHE SER PHE ILE CYS SER SER ASN ASN SEQRES 12 B 318 ASN ILE ALA ARG ILE THR GLY MET VAL GLU ARG LEU CYS SEQRES 13 B 318 GLN ALA PHE GLY PRO ARG LEU ILE GLN LEU ASP ASP VAL SEQRES 14 B 318 THR TYR HIS GLY PHE PRO ASN LEU HIS ALA LEU ALA GLY SEQRES 15 B 318 PRO GLU ALA GLU THR HIS LEU ARG LYS LEU GLY LEU GLY SEQRES 16 B 318 TYR ARG ALA ARG TYR VAL ARG ALA SER ALA LYS ALA ILE SEQRES 17 B 318 LEU GLU GLU GLN GLY GLY PRO ALA TRP LEU GLN GLN LEU SEQRES 18 B 318 ARG VAL ALA PRO TYR GLU GLU ALA HIS LYS ALA LEU CYS SEQRES 19 B 318 THR LEU PRO GLY VAL GLY ALA LYS VAL ALA ASP CYS ILE SEQRES 20 B 318 CYS LEU MET ALA LEU ASP LYS PRO GLN ALA VAL PRO VAL SEQRES 21 B 318 ASP VAL HIS VAL TRP GLN ILE ALA HIS ARG ASP TYR GLY SEQRES 22 B 318 TRP HIS PRO LYS THR SER GLN ALA LYS GLY PRO SER PRO SEQRES 23 B 318 LEU ALA ASN LYS GLU LEU GLY ASN PHE PHE ARG ASN LEU SEQRES 24 B 318 TRP GLY PRO TYR ALA GLY TRP ALA GLN ALA VAL LEU PHE SEQRES 25 B 318 SER ALA ASP LEU ARG GLN SEQRES 1 C 318 GLY SER HIS MET ARG HIS ARG THR LEU SER SER SER PRO SEQRES 2 C 318 ALA LEU TRP ALA SER ILE PRO CYS PRO ARG SER GLU LEU SEQRES 3 C 318 ARG LEU ASP LEU VAL LEU ALA SER GLY GLN SER PHE ARG SEQRES 4 C 318 TRP LYS GLU GLN SER PRO ALA HIS TRP SER GLY VAL LEU SEQRES 5 C 318 ALA ASP GLN VAL TRP THR LEU THR GLN THR GLU ASP GLN SEQRES 6 C 318 LEU TYR CYS THR VAL TYR ARG GLY ASP ASP SER GLN VAL SEQRES 7 C 318 SER ARG PRO THR LEU GLU GLU LEU GLU THR LEU HIS LYS SEQRES 8 C 318 TYR PHE GLN LEU ASP VAL SER LEU ALA GLN LEU TYR SER SEQRES 9 C 318 HIS TRP ALA SER VAL ASP SER HIS PHE GLN ARG VAL ALA SEQRES 10 C 318 GLN LYS PHE GLN GLY VAL ARG LEU LEU ARG GLN ASP PRO SEQRES 11 C 318 THR GLU CYS LEU PHE SER PHE ILE CYS SER SER ASN ASN SEQRES 12 C 318 ASN ILE ALA ARG ILE THR GLY MET VAL GLU ARG LEU CYS SEQRES 13 C 318 GLN ALA PHE GLY PRO ARG LEU ILE GLN LEU ASP ASP VAL SEQRES 14 C 318 THR TYR HIS GLY PHE PRO ASN LEU HIS ALA LEU ALA GLY SEQRES 15 C 318 PRO GLU ALA GLU THR HIS LEU ARG LYS LEU GLY LEU GLY SEQRES 16 C 318 TYR ARG ALA ARG TYR VAL ARG ALA SER ALA LYS ALA ILE SEQRES 17 C 318 LEU GLU GLU GLN GLY GLY PRO ALA TRP LEU GLN GLN LEU SEQRES 18 C 318 ARG VAL ALA PRO TYR GLU GLU ALA HIS LYS ALA LEU CYS SEQRES 19 C 318 THR LEU PRO GLY VAL GLY ALA LYS VAL ALA ASP CYS ILE SEQRES 20 C 318 CYS LEU MET ALA LEU ASP LYS PRO GLN ALA VAL PRO VAL SEQRES 21 C 318 ASP VAL HIS VAL TRP GLN ILE ALA HIS ARG ASP TYR GLY SEQRES 22 C 318 TRP HIS PRO LYS THR SER GLN ALA LYS GLY PRO SER PRO SEQRES 23 C 318 LEU ALA ASN LYS GLU LEU GLY ASN PHE PHE ARG ASN LEU SEQRES 24 C 318 TRP GLY PRO TYR ALA GLY TRP ALA GLN ALA VAL LEU PHE SEQRES 25 C 318 SER ALA ASP LEU ARG GLN HET IGQ A 401 20 HET NI A 402 1 HET IGQ B 401 20 HET IGQ C 401 20 HETNAM IGQ (7~{R})-~{N}-(4,5,6,7-TETRAHYDRO-1,2-BENZOXAZOL-3-YL) HETNAM 2 IGQ BICYCLO[4.2.0]OCTA-1,3,5-TRIENE-7-CARBOXAMIDE HETNAM NI NICKEL (II) ION FORMUL 4 IGQ 3(C16 H16 N2 O2) FORMUL 5 NI NI 2+ FORMUL 8 HOH *127(H2 O) HELIX 1 AA1 SER A 19 TRP A 23 5 5 HELIX 2 AA2 ARG A 34 LEU A 39 1 6 HELIX 3 AA3 THR A 89 PHE A 100 1 12 HELIX 4 AA4 SER A 105 SER A 115 1 11 HELIX 5 AA5 ASP A 117 PHE A 127 1 11 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 ASN A 183 ALA A 188 1 6 HELIX 9 AA9 GLU A 191 LEU A 199 1 9 HELIX 10 AB1 TYR A 203 GLU A 218 1 16 HELIX 11 AB2 PRO A 222 ALA A 231 1 10 HELIX 12 AB3 PRO A 232 CYS A 241 1 10 HELIX 13 AB4 GLY A 247 LEU A 259 1 13 HELIX 14 AB5 ASP A 268 GLY A 280 1 13 HELIX 15 AB6 SER A 292 GLY A 308 1 17 HELIX 16 AB7 TYR A 310 ARG A 324 1 15 HELIX 17 AB8 SER B 19 TRP B 23 5 5 HELIX 18 AB9 ARG B 34 LEU B 39 1 6 HELIX 19 AC1 THR B 89 PHE B 100 1 12 HELIX 20 AC2 SER B 105 ASP B 117 1 13 HELIX 21 AC3 ASP B 117 GLN B 125 1 9 HELIX 22 AC4 ASP B 136 SER B 147 1 12 HELIX 23 AC5 ASN B 151 GLY B 167 1 17 HELIX 24 AC6 ASN B 183 ALA B 188 1 6 HELIX 25 AC7 ALA B 192 GLY B 200 1 9 HELIX 26 AC8 LEU B 201 TYR B 203 5 3 HELIX 27 AC9 ARG B 204 GLU B 218 1 15 HELIX 28 AD1 PRO B 222 ALA B 231 1 10 HELIX 29 AD2 PRO B 232 THR B 242 1 11 HELIX 30 AD3 ALA B 248 ALA B 258 1 11 HELIX 31 AD4 ASP B 268 GLY B 280 1 13 HELIX 32 AD5 SER B 292 GLY B 308 1 17 HELIX 33 AD6 ALA B 311 ALA B 321 1 11 HELIX 34 AD7 SER C 19 TRP C 23 5 5 HELIX 35 AD8 ARG C 34 LEU C 39 1 6 HELIX 36 AD9 THR C 89 PHE C 100 1 12 HELIX 37 AE1 SER C 105 ASP C 117 1 13 HELIX 38 AE2 ASP C 117 GLN C 125 1 9 HELIX 39 AE3 ASP C 136 CYS C 146 1 11 HELIX 40 AE4 ASN C 151 GLY C 167 1 17 HELIX 41 AE5 ASN C 183 ALA C 188 1 6 HELIX 42 AE6 GLU C 191 GLY C 200 1 10 HELIX 43 AE7 TYR C 203 GLU C 218 1 16 HELIX 44 AE8 PRO C 222 GLN C 227 1 6 HELIX 45 AE9 PRO C 232 THR C 242 1 11 HELIX 46 AF1 GLY C 247 ALA C 258 1 12 HELIX 47 AF2 ASP C 268 GLY C 280 1 13 HELIX 48 AF3 SER C 292 GLY C 308 1 17 HELIX 49 AF4 TYR C 310 ASP C 322 1 13 SHEET 1 AA1 5 ALA A 24 PRO A 27 0 SHEET 2 AA1 5 GLN A 72 TYR A 78 -1 O CYS A 75 N ALA A 24 SHEET 3 AA1 5 GLN A 62 GLN A 68 -1 N THR A 67 O TYR 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 TRP A 47 SER A 51 -1 N LYS 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 SHEET 1 AA3 5 ALA B 24 PRO B 27 0 SHEET 2 AA3 5 GLN B 72 VAL B 77 -1 O LEU B 73 N ILE B 26 SHEET 3 AA3 5 VAL B 63 GLN B 68 -1 N THR B 67 O TYR B 74 SHEET 4 AA3 5 HIS B 54 VAL B 58 -1 N TRP B 55 O LEU B 66 SHEET 5 AA3 5 LYS B 48 SER B 51 -1 N LYS B 48 O SER B 56 SHEET 1 AA4 2 ARG B 169 LEU B 173 0 SHEET 2 AA4 2 VAL B 176 HIS B 179 -1 O VAL B 176 N LEU B 173 SHEET 1 AA5 5 ALA C 24 PRO C 27 0 SHEET 2 AA5 5 GLN C 72 TYR C 78 -1 O LEU C 73 N ILE C 26 SHEET 3 AA5 5 GLN C 62 GLN C 68 -1 N THR C 67 O TYR C 74 SHEET 4 AA5 5 HIS C 54 LEU C 59 -1 N LEU C 59 O GLN C 62 SHEET 5 AA5 5 TRP C 47 SER C 51 -1 N LYS C 48 O SER C 56 SHEET 1 AA6 2 ARG C 169 LEU C 173 0 SHEET 2 AA6 2 VAL C 176 HIS C 179 -1 O VAL C 176 N LEU C 173 LINK NE2 HIS A 276 NI NI A 402 1555 1555 2.30 LINK NE2 HIS A 282 NI NI A 402 1555 1555 2.43 LINK NI NI A 402 NE2 HIS B 276 1555 1555 2.35 LINK NI NI A 402 NE2 HIS B 282 1555 1555 2.27 LINK NI NI A 402 NE2 HIS C 276 1555 1555 2.23 LINK NI NI A 402 NE2 HIS C 282 1555 1555 2.39 CRYST1 81.459 81.533 170.145 90.00 90.00 90.00 P 21 21 21 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 0.012276 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012265 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005877 0.00000