HEADER HYDROLASE 17-MAR-25 9MBH TITLE 8-OXO-DGTP HYDROLYSIS IN HUMAN MTH1(G2K MUTANT) CRYSTAL USING MN2+: TITLE 2 THE ES-3M COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 42-197; COMPND 5 SYNONYM: MUTT HOMOLOGUE-1,2-HYDROXY-DATP DIPHOSPHATASE,8-OXO-DGTPASE, COMPND 6 NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 1,NUDIX MOTIF 1; COMPND 7 EC: 3.6.1.55,3.6.1.56; COMPND 8 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: NUDT1, MTH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDIZED PURINE NUCLEOSIDE TRIPHOSPHATE HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.HIRATA,T.NAKAMURA REVDAT 1 30-JUL-25 9MBH 0 JRNL AUTH K.HIRATA,K.FUJIMIYA,A.OSTERMANN,T.E.SCHRADER,T.HIROMOTO, JRNL AUTH 2 M.GOTO,T.ARIMORI,Y.HIRANO,K.KUSAKA,T.TAMADA,T.NAKAMURA JRNL TITL NEUTRON AND TIME-RESOLVED X-RAY CRYSTALLOGRAPHY REVEAL THE JRNL TITL 2 SUBSTRATE RECOGNITION AND CATALYTIC MECHANISM OF HUMAN NUDIX JRNL TITL 3 HYDROLASE MTH1. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 85122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 40674425 JRNL DOI 10.1073/PNAS.2510085122 REMARK 2 REMARK 2 RESOLUTION. 1.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 84605 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 4224 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 25.9600 - 3.7500 1.00 2920 151 0.1555 0.1701 REMARK 3 2 3.7500 - 2.9800 0.99 2753 148 0.1296 0.1650 REMARK 3 3 2.9800 - 2.6000 1.00 2732 158 0.1486 0.1740 REMARK 3 4 2.6000 - 2.3700 1.00 2696 168 0.1411 0.1780 REMARK 3 5 2.3700 - 2.2000 1.00 2734 140 0.1359 0.1746 REMARK 3 6 2.2000 - 2.0700 1.00 2667 155 0.1278 0.1416 REMARK 3 7 2.0700 - 1.9600 1.00 2716 133 0.1262 0.1583 REMARK 3 8 1.9600 - 1.8800 1.00 2710 148 0.1304 0.1654 REMARK 3 9 1.8800 - 1.8100 1.00 2670 151 0.1314 0.1656 REMARK 3 10 1.8100 - 1.7400 1.00 2671 135 0.1274 0.1589 REMARK 3 11 1.7400 - 1.6900 1.00 2699 143 0.1267 0.1524 REMARK 3 12 1.6900 - 1.6400 1.00 2649 166 0.1320 0.1791 REMARK 3 13 1.6400 - 1.6000 1.00 2646 139 0.1284 0.1762 REMARK 3 14 1.6000 - 1.5600 1.00 2688 151 0.1270 0.1784 REMARK 3 15 1.5600 - 1.5200 1.00 2689 140 0.1255 0.1730 REMARK 3 16 1.5200 - 1.4900 1.00 2643 126 0.1259 0.1604 REMARK 3 17 1.4900 - 1.4600 1.00 2714 130 0.1277 0.1588 REMARK 3 18 1.4600 - 1.4300 1.00 2614 143 0.1322 0.1932 REMARK 3 19 1.4300 - 1.4100 1.00 2675 119 0.1448 0.1798 REMARK 3 20 1.4100 - 1.3800 1.00 2698 134 0.1411 0.1850 REMARK 3 21 1.3800 - 1.3600 1.00 2614 148 0.1421 0.1997 REMARK 3 22 1.3600 - 1.3400 1.00 2677 138 0.1400 0.1558 REMARK 3 23 1.3400 - 1.3200 1.00 2656 131 0.1413 0.1655 REMARK 3 24 1.3200 - 1.3000 1.00 2644 141 0.1483 0.2094 REMARK 3 25 1.3000 - 1.2800 0.99 2639 129 0.1599 0.1940 REMARK 3 26 1.2800 - 1.2700 1.00 2676 134 0.1624 0.2017 REMARK 3 27 1.2700 - 1.2500 1.00 2619 123 0.1688 0.2047 REMARK 3 28 1.2500 - 1.2400 0.99 2690 124 0.1775 0.2074 REMARK 3 29 1.2400 - 1.2200 0.99 2624 125 0.1929 0.2463 REMARK 3 30 1.2200 - 1.2100 0.97 2558 153 0.2082 0.2441 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.102 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.094 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.94 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 : 0.008 2903 REMARK 3 ANGLE : 1.219 3964 REMARK 3 CHIRALITY : 0.077 407 REMARK 3 PLANARITY : 0.008 514 REMARK 3 DIHEDRAL : 16.240 1113 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 9MBH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300055937. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-15 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 : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84684 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 25.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.55600 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, CACODYLATE, NACL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 23.24400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.92300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.80600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.92300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.24400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.80600 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 60 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 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 GLN A 92 12.42 -150.82 REMARK 500 GLN A 92 34.03 -145.60 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 524 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH B 479 DISTANCE = 5.96 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 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 36 O REMARK 620 2 GLU A 56 OE2 81.0 REMARK 620 3 8DG A 201 O1B 99.1 92.9 REMARK 620 4 8DG A 201 O2A 100.6 178.1 85.8 REMARK 620 5 HOH A 312 O 168.4 90.1 73.8 88.1 REMARK 620 6 HOH A 421 O 88.6 91.0 171.8 90.0 99.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 36 O REMARK 620 2 GLU A 56 OE2 83.0 REMARK 620 3 8DG A 201 O1B 101.6 92.7 REMARK 620 4 8DG A 201 O2A 103.4 173.5 85.6 REMARK 620 5 HOH A 312 O 168.6 87.7 72.0 85.8 REMARK 620 6 HOH A 421 O 90.7 90.7 167.6 89.7 96.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 52 OE1 REMARK 620 2 GLU A 56 OE2 86.5 REMARK 620 3 8DG A 201 O1B 108.8 87.2 REMARK 620 4 HOH A 309 O 79.0 155.5 79.1 REMARK 620 5 HOH A 315 O 90.0 102.4 159.5 97.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 205 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 52 OE1 REMARK 620 2 GLU A 56 OE2 91.3 REMARK 620 3 GLU A 100 OE2 158.0 72.4 REMARK 620 4 8DG A 201 O1B 104.6 87.5 89.7 REMARK 620 5 HOH A 309 O 102.8 155.6 97.8 69.8 REMARK 620 6 HOH A 315 O 93.6 111.5 79.3 153.5 87.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 206 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 52 OE2 REMARK 620 2 8DG A 201 O2B 103.1 REMARK 620 3 HOH A 309 O 101.8 74.6 REMARK 620 4 HOH A 332 O 85.4 99.5 171.5 REMARK 620 5 HOH A 377 O 93.8 152.2 80.4 103.8 REMARK 620 6 HOH A 466 O 177.3 77.8 80.9 91.9 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 36 O REMARK 620 2 GLU B 56 OE2 85.9 REMARK 620 3 GLU B 100 OE1 159.0 74.5 REMARK 620 4 8DG B 201 O2B 103.7 100.4 73.2 REMARK 620 5 8DG B 201 O1A 105.7 168.3 93.9 76.0 REMARK 620 6 HOH B 409 O 92.5 91.3 95.4 160.6 89.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 52 OE1 REMARK 620 2 GLU B 56 OE2 93.6 REMARK 620 3 GLU B 100 OE2 164.0 77.7 REMARK 620 4 8DG B 201 O2B 112.5 88.3 81.0 REMARK 620 5 HOH B 322 O 92.4 109.9 78.2 148.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 52 OE2 REMARK 620 2 8DG B 201 O1B 94.7 REMARK 620 3 HOH B 337 O 100.5 151.8 REMARK 620 4 HOH B 374 O 80.6 99.8 106.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 52 OE1 REMARK 620 2 GLU B 56 OE2 90.0 REMARK 620 3 GLU B 100 OE2 149.0 76.5 REMARK 620 4 8DG B 201 O2B 121.5 95.7 87.9 REMARK 620 5 HOH B 322 O 82.8 99.2 72.3 151.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 206 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 52 OE2 REMARK 620 2 8DG B 201 O1G 150.8 REMARK 620 3 8DG B 201 O1B 99.7 74.4 REMARK 620 4 HOH B 337 O 87.2 105.8 165.2 REMARK 620 5 HOH B 374 O 64.7 142.4 91.4 79.6 REMARK 620 N 1 2 3 4 DBREF 9MBH A 1 156 UNP P36639 8ODP_HUMAN 42 197 DBREF 9MBH B 1 156 UNP P36639 8ODP_HUMAN 42 197 SEQADV 9MBH LYS A 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQADV 9MBH LYS B 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQRES 1 A 156 MET LYS ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 A 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 A 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 A 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 A 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 A 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 A 156 GLU LEU MET ASP VAL HIS VAL PHE CYS THR ASP SER ILE SEQRES 8 A 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO CYS SEQRES 9 A 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 A 156 PRO ASP ASP SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 A 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 A 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL SEQRES 1 B 156 MET LYS ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 B 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 B 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 B 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 B 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 B 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 B 156 GLU LEU MET ASP VAL HIS VAL PHE CYS THR ASP SER ILE SEQRES 8 B 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO CYS SEQRES 9 B 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 B 156 PRO ASP ASP SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 B 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 B 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL HET 8DG A 201 32 HET NA A 202 1 HET NA A 203 1 HET MN A 204 1 HET MN A 205 1 HET MN A 206 1 HET 8DG B 201 32 HET MN B 202 1 HET MN B 203 1 HET MN B 204 1 HET NA B 205 1 HET NA B 206 1 HETNAM 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM NA SODIUM ION HETNAM MN MANGANESE (II) ION FORMUL 3 8DG 2(C10 H16 N5 O14 P3) FORMUL 4 NA 4(NA 1+) FORMUL 6 MN 6(MN 2+) FORMUL 15 HOH *403(H2 O) HELIX 1 AA1 THR A 44 GLY A 58 1 15 HELIX 2 AA2 PRO A 112 MET A 116 5 5 HELIX 3 AA3 TRP A 117 PRO A 118 5 2 HELIX 4 AA4 ASP A 119 GLN A 129 1 11 HELIX 5 AA5 THR B 44 GLY B 58 1 15 HELIX 6 AA6 PRO B 112 MET B 116 5 5 HELIX 7 AA7 TRP B 117 PRO B 118 5 2 HELIX 8 AA8 ASP B 119 GLN B 129 1 11 SHEET 1 AA1 3 TRP A 32 ASN A 33 0 SHEET 2 AA1 3 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA1 3 MET A 101 GLN A 107 -1 O CYS A 104 N LEU A 20 SHEET 1 AA2 7 TRP A 32 ASN A 33 0 SHEET 2 AA2 7 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA2 7 SER A 4 LEU A 13 -1 N VAL A 12 O LEU A 19 SHEET 4 AA2 7 LEU A 80 THR A 88 1 O ASP A 82 N ARG A 5 SHEET 5 AA2 7 HIS A 65 PHE A 74 -1 N ILE A 70 O VAL A 83 SHEET 6 AA2 7 PHE A 133 GLN A 140 1 O PHE A 139 N GLU A 73 SHEET 7 AA2 7 THR A 144 GLU A 152 -1 O ASP A 147 N LYS A 138 SHEET 1 AA3 3 TRP B 32 ASN B 33 0 SHEET 2 AA3 3 ARG B 17 LYS B 23 -1 N GLY B 21 O ASN B 33 SHEET 3 AA3 3 MET B 101 GLN B 107 -1 O CYS B 104 N LEU B 20 SHEET 1 AA4 7 TRP B 32 ASN B 33 0 SHEET 2 AA4 7 ARG B 17 LYS B 23 -1 N GLY B 21 O ASN B 33 SHEET 3 AA4 7 SER B 4 LEU B 13 -1 N VAL B 12 O LEU B 19 SHEET 4 AA4 7 LEU B 80 GLN B 92 1 O ASP B 82 N ARG B 5 SHEET 5 AA4 7 THR B 60 PHE B 74 -1 N ALA B 63 O ASP B 89 SHEET 6 AA4 7 PHE B 133 GLN B 140 1 O PHE B 139 N GLU B 73 SHEET 7 AA4 7 THR B 144 GLU B 152 -1 O ASP B 147 N LYS B 138 LINK O GLY A 36 NA A NA A 202 1555 1555 2.23 LINK O GLY A 36 MN B MN A 204 1555 1555 2.14 LINK OE1 GLU A 52 NA A NA A 203 1555 1555 2.27 LINK OE1 GLU A 52 MN B MN A 205 1555 1555 2.24 LINK OE2 GLU A 52 MN B MN A 206 1555 1555 2.33 LINK OE2 GLU A 56 NA A NA A 202 1555 1555 2.15 LINK OE2 GLU A 56 NA A NA A 203 1555 1555 2.47 LINK OE2 GLU A 56 MN B MN A 204 1555 1555 2.15 LINK OE2 GLU A 56 MN B MN A 205 1555 1555 2.31 LINK OE2BGLU A 100 MN B MN A 205 1555 1555 2.26 LINK O1B 8DG A 201 NA A NA A 202 1555 1555 2.31 LINK O2A 8DG A 201 NA A NA A 202 1555 1555 2.15 LINK O1B 8DG A 201 NA A NA A 203 1555 1555 2.21 LINK O1B 8DG A 201 MN B MN A 204 1555 1555 2.32 LINK O2A 8DG A 201 MN B MN A 204 1555 1555 2.15 LINK O1B 8DG A 201 MN B MN A 205 1555 1555 2.37 LINK O2B 8DG A 201 MN B MN A 206 1555 1555 2.74 LINK NA A NA A 202 O HOH A 312 1555 1555 2.27 LINK NA A NA A 202 O HOH A 421 1555 1555 2.21 LINK NA A NA A 203 O AHOH A 309 1555 1555 2.76 LINK NA A NA A 203 O HOH A 315 1555 1555 2.26 LINK MN B MN A 204 O HOH A 312 1555 1555 2.36 LINK MN B MN A 204 O HOH A 421 1555 1555 2.22 LINK MN B MN A 205 O BHOH A 309 1555 1555 2.11 LINK MN B MN A 205 O HOH A 315 1555 1555 2.16 LINK MN B MN A 206 O BHOH A 309 1555 1555 2.25 LINK MN B MN A 206 O HOH A 332 1555 1555 2.15 LINK MN B MN A 206 O HOH A 377 1555 1555 2.33 LINK MN B MN A 206 O HOH A 466 1555 1555 2.51 LINK O GLY B 36 MN B MN B 202 1555 1555 2.17 LINK OE1 GLU B 52 MN B MN B 203 1555 1555 2.24 LINK OE2 GLU B 52 MN B MN B 204 1555 1555 2.43 LINK OE1 GLU B 52 NA A NA B 205 1555 1555 2.35 LINK OE2 GLU B 52 NA A NA B 206 1555 1555 2.65 LINK OE2 GLU B 56 MN B MN B 202 1555 1555 2.16 LINK OE2 GLU B 56 MN B MN B 203 1555 1555 2.33 LINK OE2 GLU B 56 NA A NA B 205 1555 1555 2.37 LINK OE1 GLU B 100 MN B MN B 202 1555 1555 2.70 LINK OE2 GLU B 100 MN B MN B 203 1555 1555 2.33 LINK OE2 GLU B 100 NA A NA B 205 1555 1555 2.35 LINK O2B 8DG B 201 MN B MN B 202 1555 1555 2.32 LINK O1A 8DG B 201 MN B MN B 202 1555 1555 2.21 LINK O2B 8DG B 201 MN B MN B 203 1555 1555 2.60 LINK O1B 8DG B 201 MN B MN B 204 1555 1555 2.73 LINK O2B 8DG B 201 NA A NA B 205 1555 1555 2.28 LINK O1G 8DG B 201 NA A NA B 206 1555 1555 3.03 LINK O1B 8DG B 201 NA A NA B 206 1555 1555 2.31 LINK MN B MN B 202 O HOH B 409 1555 1555 2.12 LINK MN B MN B 203 O HOH B 322 1555 1555 2.15 LINK MN B MN B 204 O HOH B 337 1555 1555 2.16 LINK MN B MN B 204 O HOH B 374 1555 1555 2.20 LINK NA A NA B 205 O HOH B 322 1555 1555 2.44 LINK NA A NA B 206 O HOH B 337 1555 1555 2.47 LINK NA A NA B 206 O HOH B 374 1555 1555 2.94 CRYST1 46.488 47.612 123.846 90.00 90.00 90.00 P 21 21 21 8 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 0.021511 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021003 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008075 0.00000 CONECT 614 5518 5520 CONECT 872 5519 5521 CONECT 873 5522 CONECT 939 5518 5519 5520 5521 CONECT 1729 5521 CONECT 3431 5555 CONECT 3687 5556 5558 CONECT 3688 5557 5559 CONECT 3754 5555 5556 5558 CONECT 4464 5555 CONECT 4465 5556 5558 CONECT 5486 5487 5488 5489 5490 CONECT 5487 5486 CONECT 5488 5486 CONECT 5489 5486 CONECT 5490 5486 5491 CONECT 5491 5490 5492 5493 5494 CONECT 5492 5491 5518 5519 5520 CONECT 5492 5521 CONECT 5493 5491 5522 CONECT 5494 5491 5495 CONECT 5495 5494 5496 5497 5498 CONECT 5496 5495 CONECT 5497 5495 5518 5520 CONECT 5498 5495 5499 CONECT 5499 5498 5500 CONECT 5500 5499 5501 5502 CONECT 5501 5500 5505 CONECT 5502 5500 5503 5504 CONECT 5503 5502 CONECT 5504 5502 5505 CONECT 5505 5501 5504 5506 CONECT 5506 5505 5507 5516 CONECT 5507 5506 5508 5517 CONECT 5508 5507 5509 CONECT 5509 5508 5510 5516 CONECT 5510 5509 5511 5512 CONECT 5511 5510 CONECT 5512 5510 5513 CONECT 5513 5512 5514 5515 CONECT 5514 5513 CONECT 5515 5513 5516 CONECT 5516 5506 5509 5515 CONECT 5517 5507 CONECT 5518 614 939 5492 5497 CONECT 5518 5572 5689 CONECT 5519 872 939 5492 5568 CONECT 5519 5575 CONECT 5520 614 939 5492 5497 CONECT 5520 5572 5689 CONECT 5521 872 939 1729 5492 CONECT 5521 5569 5575 CONECT 5522 873 5493 5569 5593 CONECT 5522 5640 5734 CONECT 5523 5524 5525 5526 5527 CONECT 5524 5523 5559 CONECT 5525 5523 CONECT 5526 5523 CONECT 5527 5523 5528 CONECT 5528 5527 5529 5530 5531 CONECT 5529 5528 5557 5559 CONECT 5530 5528 5555 5556 5558 CONECT 5531 5528 5532 CONECT 5532 5531 5533 5534 5535 CONECT 5533 5532 5555 CONECT 5534 5532 CONECT 5535 5532 5536 CONECT 5536 5535 5537 CONECT 5537 5536 5538 5539 CONECT 5538 5537 5542 CONECT 5539 5537 5540 5541 CONECT 5540 5539 CONECT 5541 5539 5542 CONECT 5542 5538 5541 5543 CONECT 5543 5542 5544 5553 CONECT 5544 5543 5545 5554 CONECT 5545 5544 5546 CONECT 5546 5545 5547 5553 CONECT 5547 5546 5548 5549 CONECT 5548 5547 CONECT 5549 5547 5550 CONECT 5550 5549 5551 5552 CONECT 5551 5550 CONECT 5552 5550 5553 CONECT 5553 5543 5546 5552 CONECT 5554 5544 CONECT 5555 3431 3754 4464 5530 CONECT 5555 5533 5907 CONECT 5556 3687 3754 4465 5530 CONECT 5556 5818 CONECT 5557 3688 5529 5833 5872 CONECT 5558 3687 3754 4465 5530 CONECT 5558 5818 CONECT 5559 3688 5524 5529 5833 CONECT 5559 5872 CONECT 5568 5519 CONECT 5569 5521 5522 CONECT 5572 5518 5520 CONECT 5575 5519 5521 CONECT 5593 5522 CONECT 5640 5522 CONECT 5689 5518 5520 CONECT 5734 5522 CONECT 5818 5556 5558 CONECT 5833 5557 5559 CONECT 5872 5557 5559 CONECT 5907 5555 MASTER 374 0 12 8 20 0 0 6 3019 2 107 24 END