HEADER HYDROLASE 13-JAN-23 8I1E TITLE CRYSTAL STRUCTURE OF HUMAN MTH1(G2K MUTANT) IN COMPLEX WITH 2-OXO-DATP TITLE 2 AT PH 8.0 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 NUDIX HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAMURA,Y.YAMAGATA REVDAT 3 29-MAY-24 8I1E 1 REMARK REVDAT 2 26-JUL-23 8I1E 1 JRNL REVDAT 1 22-MAR-23 8I1E 0 JRNL AUTH T.NAKAMURA,Y.KOGA-OGAWA,K.FUJIMIYA,M.CHIRIFU,M.GOTO, JRNL AUTH 2 S.IKEMIZU,Y.NAKABEPPU,Y.YAMAGATA JRNL TITL PROTONATION STATES OF ASP RESIDUES IN THE HUMAN NUDIX JRNL TITL 2 HYDROLASE MTH1 CONTRIBUTE TO ITS BROAD SUBSTRATE JRNL TITL 3 RECOGNITION. JRNL REF FEBS LETT. V. 597 1770 2023 JRNL REFN ISSN 0014-5793 JRNL PMID 36914375 JRNL DOI 10.1002/1873-3468.14611 REMARK 2 REMARK 2 RESOLUTION. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 108606 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5543 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 33.1900 - 3.4100 1.00 3904 155 0.1687 0.2175 REMARK 3 2 3.4100 - 2.7000 0.99 3664 203 0.1511 0.1761 REMARK 3 3 2.7000 - 2.3600 1.00 3641 196 0.1510 0.1803 REMARK 3 4 2.3600 - 2.1500 1.00 3664 158 0.1358 0.1585 REMARK 3 5 2.1500 - 1.9900 0.99 3605 185 0.1268 0.1386 REMARK 3 6 1.9900 - 1.8700 0.99 3587 196 0.1239 0.1678 REMARK 3 7 1.8700 - 1.7800 0.99 3555 189 0.1239 0.1641 REMARK 3 8 1.7800 - 1.7000 0.99 3521 191 0.1268 0.1521 REMARK 3 9 1.7000 - 1.6400 0.99 3549 216 0.1270 0.1817 REMARK 3 10 1.6400 - 1.5800 0.99 3474 209 0.1188 0.1656 REMARK 3 11 1.5800 - 1.5300 0.99 3534 208 0.1224 0.1441 REMARK 3 12 1.5300 - 1.4900 0.98 3455 204 0.1220 0.1685 REMARK 3 13 1.4900 - 1.4500 0.98 3492 195 0.1226 0.1731 REMARK 3 14 1.4500 - 1.4100 0.98 3490 183 0.1271 0.1811 REMARK 3 15 1.4100 - 1.3800 0.98 3473 201 0.1290 0.1600 REMARK 3 16 1.3800 - 1.3500 0.98 3446 213 0.1273 0.1671 REMARK 3 17 1.3500 - 1.3200 0.97 3412 193 0.1324 0.1847 REMARK 3 18 1.3200 - 1.3000 0.97 3435 234 0.1328 0.1766 REMARK 3 19 1.3000 - 1.2800 0.97 3456 165 0.1386 0.1835 REMARK 3 20 1.2800 - 1.2500 0.97 3426 149 0.1389 0.1737 REMARK 3 21 1.2500 - 1.2300 0.97 3485 169 0.1362 0.1708 REMARK 3 22 1.2300 - 1.2200 0.97 3429 165 0.1405 0.1778 REMARK 3 23 1.2200 - 1.2000 0.96 3415 184 0.1437 0.1970 REMARK 3 24 1.2000 - 1.1800 0.96 3376 177 0.1448 0.1625 REMARK 3 25 1.1800 - 1.1700 0.94 3300 177 0.1463 0.1743 REMARK 3 26 1.1700 - 1.1500 0.92 3293 174 0.1606 0.2043 REMARK 3 27 1.1500 - 1.1400 0.90 3205 162 0.1683 0.2145 REMARK 3 28 1.1400 - 1.1200 0.89 3126 165 0.1818 0.1887 REMARK 3 29 1.1200 - 1.1100 0.86 3026 164 0.1939 0.2131 REMARK 3 30 1.1100 - 1.1000 0.74 2625 163 0.2479 0.2239 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) : 0.085 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.428 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.77 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 3005 REMARK 3 ANGLE : 1.211 4120 REMARK 3 CHIRALITY : 0.078 420 REMARK 3 PLANARITY : 0.008 532 REMARK 3 DIHEDRAL : 17.663 1145 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 8I1E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-17 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-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 108617 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 33.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32400 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 (%): 35.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, TRIS, NACL, VAPOR REMARK 280 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 23.11600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.00350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.83800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.00350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.11600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.83800 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: 270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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: 290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 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 B 26 REMARK 465 PHE B 27 REMARK 465 GLY B 28 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 HZ1 LYS A 66 O HOH A 301 1.57 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 CYS B 87 CB CYS B 87 SG -0.103 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 ASP A 89 -64.66 -103.76 REMARK 500 GLN A 92 18.38 -147.40 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 492 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 493 DISTANCE = 8.06 ANGSTROMS REMARK 525 HOH B 467 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH B 468 DISTANCE = 6.69 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 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 36 O REMARK 620 2 GLU A 56 OE2 79.0 REMARK 620 3 6U4 A 201 O1B 106.7 93.6 REMARK 620 4 6U4 A 201 O2A 108.1 170.2 78.0 REMARK 620 5 HOH A 373 O 80.9 89.2 172.3 98.5 REMARK 620 6 HOH A 448 O 162.9 87.1 83.9 87.0 89.1 REMARK 620 N 1 2 3 4 5 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 GLU A 52 OE2 REMARK 620 2 6U4 A 201 O2B 102.1 REMARK 620 3 HOH A 384 O 81.3 103.4 REMARK 620 4 HOH A 416 O 116.4 116.2 129.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 52 OE1 REMARK 620 2 GLU A 56 OE2 91.2 REMARK 620 3 6U4 A 201 O1B 117.3 100.0 REMARK 620 4 HOH A 302 O 149.2 110.9 80.8 REMARK 620 5 HOH A 303 O 78.9 109.5 146.2 73.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 36 O REMARK 620 2 6U4 B 201 O2B 110.8 REMARK 620 3 6U4 B 201 O1A 105.2 76.9 REMARK 620 4 HOH B 326 O 74.6 172.5 96.8 REMARK 620 5 HOH B 358 O 157.9 70.7 96.6 106.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 36 O REMARK 620 2 GLU B 52 OE1 84.8 REMARK 620 3 GLU B 56 OE2 84.8 98.2 REMARK 620 4 HOH B 358 O 120.2 141.7 59.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 52 OE1 REMARK 620 2 6U4 B 201 O2B 123.5 REMARK 620 3 HOH B 306 O 84.6 74.5 REMARK 620 4 HOH B 393 O 79.2 148.2 87.4 REMARK 620 5 HOH B 434 O 106.6 96.6 47.5 52.9 REMARK 620 N 1 2 3 4 DBREF 8I1E A 1 156 UNP P36639 8ODP_HUMAN 42 197 DBREF 8I1E B 1 156 UNP P36639 8ODP_HUMAN 42 197 SEQADV 8I1E LYS A 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQADV 8I1E 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 6U4 A 201 39 HET NA A 202 1 HET NA A 203 1 HET NA A 204 1 HET 6U4 B 201 62 HET NA B 202 2 HET NA B 203 1 HETNAM 6U4 [[(2R,3S,5R)-5-(6-AZANYL-2-OXIDANYLIDENE-1H-PURIN-9- HETNAM 2 6U4 YL)-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL- HETNAM 3 6U4 PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE HETNAM NA SODIUM ION HETSYN 6U4 2-OXO-DATP FORMUL 3 6U4 2(C10 H16 N5 O13 P3) FORMUL 4 NA 5(NA 1+) FORMUL 10 HOH *361(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 ARG A 102 N MET A 22 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 LYS A 132 GLN A 140 1 O PHE A 139 N GLU A 73 SHEET 7 AA2 7 THR A 144 VAL A 153 -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 PHE B 106 -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 GLN B 14 -1 N GLN B 14 O ARG B 17 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 ILE B 70 O VAL B 83 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 NA A 203 1555 1555 2.38 LINK OE2 GLU A 52 NA B NA A 202 1555 1555 2.41 LINK OE1 GLU A 52 NA NA A 204 1555 1555 2.32 LINK OE2BGLU A 56 NA NA A 203 1555 1555 2.26 LINK OE2BGLU A 56 NA NA A 204 1555 1555 2.23 LINK O2BB6U4 A 201 NA B NA A 202 1555 1555 2.40 LINK O1BA6U4 A 201 NA NA A 203 1555 1555 2.47 LINK O2A 6U4 A 201 NA NA A 203 1555 1555 2.33 LINK O1BA6U4 A 201 NA NA A 204 1555 1555 2.28 LINK NA B NA A 202 O HOH A 384 1555 1555 2.35 LINK NA B NA A 202 O BHOH A 416 1555 1555 2.78 LINK NA NA A 203 O HOH A 373 1555 1555 2.38 LINK NA NA A 203 O HOH A 448 1555 1555 2.33 LINK NA NA A 204 O HOH A 302 1555 1555 2.42 LINK NA NA A 204 O HOH A 303 1555 1555 2.69 LINK O GLY B 36 NA A NA B 202 1555 1555 2.41 LINK O GLY B 36 NA B NA B 202 1555 1555 2.46 LINK OE1 GLU B 52 NA B NA B 202 1555 1555 2.53 LINK OE1 GLU B 52 NA A NA B 203 1555 1555 2.22 LINK OE2BGLU B 56 NA B NA B 202 1555 1555 2.21 LINK O2BA6U4 B 201 NA A NA B 202 1555 1555 2.55 LINK O1AA6U4 B 201 NA A NA B 202 1555 1555 2.13 LINK O2BA6U4 B 201 NA A NA B 203 1555 1555 2.52 LINK NA A NA B 202 O HOH B 326 1555 1555 2.21 LINK NA A NA B 202 O HOH B 358 1555 1555 2.54 LINK NA B NA B 202 O HOH B 358 1555 1555 3.12 LINK NA A NA B 203 O AHOH B 306 1555 1555 2.81 LINK NA A NA B 203 O HOH B 393 1555 1555 2.33 LINK NA A NA B 203 O HOH B 434 1555 1555 2.93 CRYST1 46.232 47.676 124.007 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 0.021630 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020975 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008064 0.00000