HEADER HYDROLASE/DNA 30-JUL-22 8DVY TITLE DNA GLYCOSYLASE MUTY VARIANT N146S IN COMPLEX WITH DNA CONTAINING D(8- TITLE 2 OXO-G) PAIRED WITH AN ENZYME-GENERATED ABASIC SITE PRODUCT (AP) AND TITLE 3 CRYSTALIZED WITH CALCIUM ACETATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OXOG:A-SPECIFIC ADENINE GLYCOSYLASE; COMPND 5 EC: 3.2.2.31; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*TP*GP*TP*CP*CP*AP*(AAB)P*GP*TP*CP*T)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: MUTY; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-DNA COMPLEX, DNA REPAIR, APURINIC/APYRIMIDINIC, BASE EXCISION KEYWDS 2 REPAIR, HYDROLASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.DEMIR,L.P.RUSSELBURG,M.P.HORVATH,S.S.DAVID REVDAT 3 25-OCT-23 8DVY 1 REMARK REVDAT 2 03-MAY-23 8DVY 1 JRNL REVDAT 1 30-NOV-22 8DVY 0 JRNL AUTH M.DEMIR,L.P.RUSSELBURG,W.J.LIN,C.H.TRASVINA-ARENAS,B.HUANG, JRNL AUTH 2 P.K.YUEN,M.P.HORVATH,S.S.DAVID JRNL TITL STRUCTURAL SNAPSHOTS OF BASE EXCISION BY THE JRNL TITL 2 CANCER-ASSOCIATED VARIANT MUTY N146S REVEAL A RETAINING JRNL TITL 3 MECHANISM. JRNL REF NUCLEIC ACIDS RES. V. 51 1034 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36631987 JRNL DOI 10.1093/NAR/GKAC1246 REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 36226 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.420 REMARK 3 FREE R VALUE TEST SET COUNT : 878 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 70.3500 - 4.2900 1.00 5902 144 0.1873 0.2357 REMARK 3 2 4.2900 - 3.4000 1.00 5898 137 0.2279 0.2419 REMARK 3 3 3.4000 - 2.9700 1.00 5908 145 0.3051 0.2980 REMARK 3 4 2.9700 - 2.7000 1.00 5844 162 0.3403 0.3486 REMARK 3 5 2.7000 - 2.5100 1.00 5915 147 0.3446 0.3534 REMARK 3 6 2.5100 - 2.3600 1.00 5881 143 0.3810 0.3856 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.456 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.883 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 3239 REMARK 3 ANGLE : 0.904 4515 REMARK 3 CHIRALITY : 0.047 508 REMARK 3 PLANARITY : 0.006 508 REMARK 3 DIHEDRAL : 18.232 1177 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8DVY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267459. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-21 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 : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36236 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 REMARK 200 RESOLUTION RANGE LOW (A) : 70.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.23700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 0.0681 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 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 <I/SIGMA(I)> 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: PHENIX REMARK 200 STARTING MODEL: 8DVP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, CALCIUM ACETATE, ETHYLENE REMARK 280 GLYCOL, TRIS.HCL, B-MERCAPTOETHANOL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293.13K 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 18.93000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.35500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.74000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.35500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.93000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.74000 REMARK 290 SMTRY3 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 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 THR A 2 REMARK 465 ARG A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 GLY A 275 REMARK 465 TYR A 290 REMARK 465 GLY A 291 REMARK 465 GLY A 361 REMARK 465 VAL A 362 REMARK 465 ARG A 363 REMARK 465 ARG A 364 REMARK 465 PRO A 365 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 ARG A 7 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 ARG A 15 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 34 NE CZ NH1 NH2 REMARK 470 GLU A 52 CG CD OE1 OE2 REMARK 470 GLU A 76 CG CD OE1 OE2 REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 ARG A 119 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 LYS A 163 CE NZ REMARK 470 GLN A 172 CG CD OE1 NE2 REMARK 470 GLU A 176 CG CD OE1 OE2 REMARK 470 ARG A 201 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 202 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 211 CG CD OE1 NE2 REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 MET A 229 SD CE REMARK 470 LYS A 230 CD CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 GLU A 248 CG CD OE1 OE2 REMARK 470 ASN A 264 OD1 ND2 REMARK 470 ASP A 277 CG OD1 OD2 REMARK 470 LYS A 279 CG CD CE NZ REMARK 470 GLU A 280 CG CD OE1 OE2 REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 GLN A 284 CG CD OE1 NE2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 GLN A 289 CG CD OE1 NE2 REMARK 470 LEU A 292 CG CD1 CD2 REMARK 470 GLN A 293 CG CD OE1 NE2 REMARK 470 GLU A 295 CG CD OE1 OE2 REMARK 470 GLU A 298 CD OE1 OE2 REMARK 470 ARG A 320 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 328 CG CD OE1 OE2 REMARK 470 GLU A 329 CD OE1 OE2 REMARK 470 ASP A 337 CG OD1 OD2 REMARK 470 LYS A 340 CE NZ REMARK 470 LYS A 356 CG CD CE NZ REMARK 470 DT C 12 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT C 12 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT C 12 C7 C6 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 H4' AAB C 18 CA CA C 101 1.59 REMARK 500 N7 DA C 17 O HOH C 201 2.14 REMARK 500 REMARK 500 REMARK: NULL 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 DT C 12 O3' DG C 13 P -0.121 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 DC B 5 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 16 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES 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 262 56.13 38.68 REMARK 500 THR A 273 74.43 -104.99 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 A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 118 O REMARK 620 2 SER A 118 OG 72.2 REMARK 620 3 VAL A 123 O 97.1 90.6 REMARK 620 4 HOH A 510 O 73.1 143.6 83.2 REMARK 620 5 HOH A 512 O 144.0 72.3 89.3 142.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 144 OD2 REMARK 620 2 SER A 146 OG 98.4 REMARK 620 3 HOH A 509 O 95.7 65.6 REMARK 620 4 AAB C 18 O4' 70.8 129.9 67.1 REMARK 620 5 AAB C 18 O3' 54.9 145.8 130.9 66.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 198 SG REMARK 620 2 SF4 A 401 S1 118.3 REMARK 620 3 SF4 A 401 S2 113.4 106.1 REMARK 620 4 SF4 A 401 S4 110.3 103.0 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 SF4 A 401 S1 105.4 REMARK 620 3 SF4 A 401 S3 126.9 104.6 REMARK 620 4 SF4 A 401 S4 110.0 103.4 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 SF4 A 401 S2 120.1 REMARK 620 3 SF4 A 401 S3 110.2 103.7 REMARK 620 4 SF4 A 401 S4 112.7 104.8 103.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 214 SG REMARK 620 2 SF4 A 401 S1 102.3 REMARK 620 3 SF4 A 401 S2 124.0 105.8 REMARK 620 4 SF4 A 401 S3 115.2 104.0 103.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 404 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 257 OD2 REMARK 620 2 THR A 259 O 130.2 REMARK 620 3 THR A 259 OG1 119.5 63.8 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8DVP RELATED DB: PDB DBREF 8DVY A 1 365 UNP P83847 MUTY_GEOSE 1 365 DBREF 8DVY B 1 11 PDB 8DVY 8DVY 1 11 DBREF 8DVY C 12 22 PDB 8DVY 8DVY 12 22 SEQADV 8DVY SER A 146 UNP P83847 ASN 146 ENGINEERED MUTATION SEQRES 1 A 365 MET THR ARG GLU THR GLU ARG PHE PRO ALA ARG GLU PHE SEQRES 2 A 365 GLN ARG ASP LEU LEU ASP TRP PHE ALA ARG GLU ARG ARG SEQRES 3 A 365 ASP LEU PRO TRP ARG LYS ASP ARG ASP PRO TYR LYS VAL SEQRES 4 A 365 TRP VAL SER GLU VAL MET LEU GLN GLN THR ARG VAL GLU SEQRES 5 A 365 THR VAL ILE PRO TYR PHE GLU GLN PHE ILE ASP ARG PHE SEQRES 6 A 365 PRO THR LEU GLU ALA LEU ALA ASP ALA ASP GLU ASP GLU SEQRES 7 A 365 VAL LEU LYS ALA TRP GLU GLY LEU GLY TYR TYR SER ARG SEQRES 8 A 365 VAL ARG ASN LEU HIS ALA ALA VAL LYS GLU VAL LYS THR SEQRES 9 A 365 ARG TYR GLY GLY LYS VAL PRO ASP ASP PRO ASP GLU PHE SEQRES 10 A 365 SER ARG LEU LYS GLY VAL GLY PRO TYR THR VAL GLY ALA SEQRES 11 A 365 VAL LEU SER LEU ALA TYR GLY VAL PRO GLU PRO ALA VAL SEQRES 12 A 365 ASP GLY SER VAL MET ARG VAL LEU SER ARG LEU PHE LEU SEQRES 13 A 365 VAL THR ASP ASP ILE ALA LYS PRO SER THR ARG LYS ARG SEQRES 14 A 365 PHE GLU GLN ILE VAL ARG GLU ILE MET ALA TYR GLU ASN SEQRES 15 A 365 PRO GLY ALA PHE ASN GLU ALA LEU ILE GLU LEU GLY ALA SEQRES 16 A 365 LEU VAL CYS THR PRO ARG ARG PRO SER CYS LEU LEU CYS SEQRES 17 A 365 PRO VAL GLN ALA TYR CYS GLN ALA PHE ALA GLU GLY VAL SEQRES 18 A 365 ALA GLU GLU LEU PRO VAL LYS MET LYS LYS THR ALA VAL SEQRES 19 A 365 LYS GLN VAL PRO LEU ALA VAL ALA VAL LEU ALA ASP ASP SEQRES 20 A 365 GLU GLY ARG VAL LEU ILE ARG LYS ARG ASP SER THR GLY SEQRES 21 A 365 LEU LEU ALA ASN LEU TRP GLU PHE PRO SER CYS GLU THR SEQRES 22 A 365 ASP GLY ALA ASP GLY LYS GLU LYS LEU GLU GLN MET VAL SEQRES 23 A 365 GLY GLU GLN TYR GLY LEU GLN VAL GLU LEU THR GLU PRO SEQRES 24 A 365 ILE VAL SER PHE GLU HIS ALA PHE SER HIS LEU VAL TRP SEQRES 25 A 365 GLN LEU THR VAL PHE PRO GLY ARG LEU VAL HIS GLY GLY SEQRES 26 A 365 PRO VAL GLU GLU PRO TYR ARG LEU ALA PRO GLU ASP GLU SEQRES 27 A 365 LEU LYS ALA TYR ALA PHE PRO VAL SER HIS GLN ARG VAL SEQRES 28 A 365 TRP ARG GLU TYR LYS GLU TRP ALA SER GLY VAL ARG ARG SEQRES 29 A 365 PRO SEQRES 1 B 11 DA DA DG DA DC 8OG DT DG DG DA DC SEQRES 1 C 11 DT DG DT DC DC DA AAB DG DT DC DT HET 8OG B 6 34 HET AAB C 18 20 HET SF4 A 401 8 HET ACT A 402 7 HET CA A 403 1 HET CA A 404 1 HET CA C 101 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM AAB 2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM ACT ACETATE ION HETNAM CA CALCIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN AAB ABASIC DEOXYRIBOSE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 3 AAB C5 H11 O7 P FORMUL 4 SF4 FE4 S4 FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 CA 3(CA 2+) FORMUL 9 HOH *24(H2 O) HELIX 1 AA1 PRO A 9 ARG A 25 1 17 HELIX 2 AA2 LEU A 28 LYS A 32 5 5 HELIX 3 AA3 ASP A 35 LEU A 46 1 12 HELIX 4 AA4 ARG A 50 PHE A 65 1 16 HELIX 5 AA5 THR A 67 ASP A 73 1 7 HELIX 6 AA6 ASP A 75 GLU A 84 1 10 HELIX 7 AA7 TYR A 89 ARG A 105 1 17 HELIX 8 AA8 ASP A 113 SER A 118 1 6 HELIX 9 AA9 GLY A 124 TYR A 136 1 13 HELIX 10 AB1 ASP A 144 PHE A 155 1 12 HELIX 11 AB2 LYS A 163 MET A 178 1 16 HELIX 12 AB3 ASN A 182 VAL A 197 1 16 HELIX 13 AB4 SER A 204 CYS A 208 5 5 HELIX 14 AB5 VAL A 210 TYR A 213 5 4 HELIX 15 AB6 CYS A 214 GLY A 220 1 7 HELIX 16 AB7 VAL A 221 LEU A 225 5 5 HELIX 17 AB8 ASP A 277 GLN A 289 1 13 HELIX 18 AB9 PRO A 335 LYS A 340 1 6 HELIX 19 AC1 PRO A 345 SER A 360 1 16 SHEET 1 AA1 4 SER A 270 GLU A 272 0 SHEET 2 AA1 4 LYS A 235 ALA A 245 -1 N ALA A 240 O CYS A 271 SHEET 3 AA1 4 LEU A 310 VAL A 322 1 O VAL A 311 N VAL A 237 SHEET 4 AA1 4 GLN A 293 LEU A 296 -1 N GLN A 293 O VAL A 322 SHEET 1 AA2 4 SER A 270 GLU A 272 0 SHEET 2 AA2 4 LYS A 235 ALA A 245 -1 N ALA A 240 O CYS A 271 SHEET 3 AA2 4 LEU A 310 VAL A 322 1 O VAL A 311 N VAL A 237 SHEET 4 AA2 4 VAL A 301 ALA A 306 -1 N HIS A 305 O TRP A 312 SHEET 1 AA3 3 TRP A 266 GLU A 267 0 SHEET 2 AA3 3 VAL A 251 LYS A 255 -1 N ARG A 254 O GLU A 267 SHEET 3 AA3 3 TYR A 331 ALA A 334 -1 O ALA A 334 N VAL A 251 LINK O3' DC B 5 P 8OG B 6 1555 1555 1.60 LINK O3' 8OG B 6 P DT B 7 1555 1555 1.60 LINK O3' DA C 17 P AAB C 18 1555 1555 1.60 LINK O3' AAB C 18 P DG C 19 1555 1555 1.63 LINK O SER A 118 CA CA A 403 1555 1555 2.35 LINK OG SER A 118 CA CA A 403 1555 1555 2.61 LINK O VAL A 123 CA CA A 403 1555 1555 2.28 LINK OD2 ASP A 144 CA CA C 101 1555 1555 2.69 LINK OG SER A 146 CA CA C 101 1555 1555 2.45 LINK SG CYS A 198 FE3 SF4 A 401 1555 1555 2.45 LINK SG CYS A 205 FE2 SF4 A 401 1555 1555 2.04 LINK SG CYS A 208 FE1 SF4 A 401 1555 1555 2.30 LINK SG CYS A 214 FE4 SF4 A 401 1555 1555 2.18 LINK OD2 ASP A 257 CA CA A 404 1555 1555 2.66 LINK O THR A 259 CA CA A 404 1555 1555 2.59 LINK OG1 THR A 259 CA CA A 404 1555 1555 2.71 LINK CA CA A 403 O HOH A 510 1555 1555 2.30 LINK CA CA A 403 O HOH A 512 1555 1555 2.00 LINK O HOH A 509 CA CA C 101 1555 1555 2.63 LINK O4' AAB C 18 CA CA C 101 1555 1555 2.65 LINK O3' AAB C 18 CA CA C 101 1555 1555 3.08 CISPEP 1 LEU A 225 PRO A 226 0 -2.71 CISPEP 2 GLU A 329 PRO A 330 0 3.11 CRYST1 37.860 85.480 140.710 90.00 90.00 90.00 P 21 21 21 4 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 0.026413 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007107 0.00000