HEADER HYDROLASE 06-APR-05 1ZAB TITLE CRYSTAL STRUCTURE OF MOUSE CYTIDINE DEAMINASE COMPLEXED WITH 3- TITLE 2 DEAZAURIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTIDINE DEAMINASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 3.5.4.5; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-21C KEYWDS MOUSE, CYTIDINE DEAMINASE, ZINC, 3-DEAZAURIDINE, SUBSTRATE KEYWDS 2 DISSOCIATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.H.TEH REVDAT 4 25-OCT-23 1ZAB 1 REMARK LINK REVDAT 3 24-FEB-09 1ZAB 1 VERSN REVDAT 2 11-JUL-06 1ZAB 1 JRNL REVDAT 1 11-APR-06 1ZAB 0 JRNL AUTH A.H.TEH,M.KIMURA,M.YAMAMOTO,N.TANAKA,I.YAMAGUCHI,T.KUMASAKA JRNL TITL THE 1.48 A RESOLUTION CRYSTAL STRUCTURE OF THE JRNL TITL 2 HOMOTETRAMERIC CYTIDINE DEAMINASE FROM MOUSE JRNL REF BIOCHEMISTRY V. 45 7825 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16784234 JRNL DOI 10.1021/BI060345F REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 91083.180 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 28184 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 SET) : 0.176 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1368 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4393 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE : 0.2280 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 204 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 309 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.52000 REMARK 3 B22 (A**2) : 6.01000 REMARK 3 B33 (A**2) : -5.49000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.180 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.870 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.350 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.090 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 47.52 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : URD.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : URD.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISORDERED ATOMS WERE REFINED WITH ZERO REMARK 3 OCCUPANCY. REMARK 4 REMARK 4 1ZAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032495. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BBS REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28544 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 REMARK 200 RESOLUTION RANGE LOW (A) : 48.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.210 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 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) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.28 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2FR5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, CITRATE, PH 4.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.11850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.18050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 90.26550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.11850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.18050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 90.26550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.11850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.18050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 90.26550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.11850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.18050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 90.26550 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS SIMILAR TO THE TETRAMER REMARK 300 CONTAINED IN THE ASYMMETRIC UNIT 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -240.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 28410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -498.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 BIOMT1 2 -1.000000 0.000000 0.000000 82.23700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A1005 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 GLU A 4 REMARK 465 ARG A 5 REMARK 465 PRO A 6 REMARK 465 SER A 7 REMARK 465 CYS A 8 REMARK 465 ALA A 9 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLN B 3 REMARK 465 GLU B 4 REMARK 465 ARG B 5 REMARK 465 PRO B 6 REMARK 465 SER B 7 REMARK 465 CYS B 8 REMARK 465 ALA B 9 REMARK 465 LYS B 144 REMARK 465 ILE B 145 REMARK 465 GLN B 146 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 GLN C 3 REMARK 465 GLU C 4 REMARK 465 ARG C 5 REMARK 465 PRO C 6 REMARK 465 SER C 7 REMARK 465 CYS C 8 REMARK 465 ILE C 145 REMARK 465 GLN C 146 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 GLN D 3 REMARK 465 GLU D 4 REMARK 465 ARG D 5 REMARK 465 PRO D 6 REMARK 465 SER D 7 REMARK 465 CYS D 8 REMARK 465 ALA D 9 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 VAL A 10 CB CG1 CG2 REMARK 480 GLU B 11 CB CG CD OE1 OE2 REMARK 480 ASP B 112 CG OD1 OD2 REMARK 480 GLU B 140 CD OE1 OE2 REMARK 480 GLU C 11 CG CD OE1 OE2 REMARK 480 ARG C 35 NE CZ NH1 NH2 REMARK 480 ASP C 112 CG OD1 OD2 REMARK 480 GLN C 143 CG CD OE1 NE2 REMARK 480 LYS C 144 CE NZ REMARK 480 GLU D 13 OE1 OE2 REMARK 480 GLU D 93 CB CG CD OE1 OE2 REMARK 480 ASP D 112 OD1 OD2 REMARK 480 LYS D 144 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 ASP A 112 50.33 -93.78 REMARK 500 CYS B 31 56.20 -140.26 REMARK 500 CYS C 31 59.42 -145.08 REMARK 500 GLU C 93 45.36 -100.65 REMARK 500 CYS D 31 55.53 -141.07 REMARK 500 GLU D 93 61.11 -117.73 REMARK 500 GLU D 94 124.49 -176.88 REMARK 500 ASP D 112 37.71 -93.57 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 ZN A 147 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 CYS A 99 SG 115.4 REMARK 620 3 CYS A 102 SG 110.2 114.4 REMARK 620 4 HOH A1006 O 113.9 103.2 98.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 147 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 65 SG REMARK 620 2 CYS B 99 SG 112.0 REMARK 620 3 CYS B 102 SG 108.5 117.5 REMARK 620 4 HOH B1003 O 109.9 104.6 103.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 147 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 65 SG REMARK 620 2 CYS C 99 SG 117.4 REMARK 620 3 CYS C 102 SG 108.4 114.6 REMARK 620 4 HOH C1004 O 112.9 103.2 98.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 147 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 65 SG REMARK 620 2 CYS D 99 SG 113.7 REMARK 620 3 CYS D 102 SG 107.7 115.8 REMARK 620 4 HOH D1005 O 111.0 108.6 99.1 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URD A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URD B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URD C 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URD D 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FR5 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH TETRAHYDROURIDINE. REMARK 900 RELATED ID: 2FR6 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH CYTIDINE. DBREF 1ZAB A 1 146 UNP P56389 CDD_MOUSE 1 146 DBREF 1ZAB B 1 146 UNP P56389 CDD_MOUSE 1 146 DBREF 1ZAB C 1 146 UNP P56389 CDD_MOUSE 1 146 DBREF 1ZAB D 1 146 UNP P56389 CDD_MOUSE 1 146 SEQRES 1 A 146 MET ALA GLN GLU ARG PRO SER CYS ALA VAL GLU PRO GLU SEQRES 2 A 146 HIS VAL GLN ARG LEU LEU LEU SER SER ARG GLU ALA LYS SEQRES 3 A 146 LYS SER ALA TYR CYS PRO TYR SER ARG PHE PRO VAL GLY SEQRES 4 A 146 ALA ALA LEU LEU THR GLY ASP GLY ARG ILE PHE SER GLY SEQRES 5 A 146 CYS ASN ILE GLU ASN ALA CYS TYR PRO LEU GLY VAL CYS SEQRES 6 A 146 ALA GLU ARG THR ALA ILE GLN LYS ALA ILE SER GLU GLY SEQRES 7 A 146 TYR LYS ASP PHE ARG ALA ILE ALA ILE SER SER ASP LEU SEQRES 8 A 146 GLN GLU GLU PHE ILE SER PRO CYS GLY ALA CYS ARG GLN SEQRES 9 A 146 VAL MET ARG GLU PHE GLY THR ASP TRP ALA VAL TYR MET SEQRES 10 A 146 THR LYS PRO ASP GLY THR PHE VAL VAL ARG THR VAL GLN SEQRES 11 A 146 GLU LEU LEU PRO ALA SER PHE GLY PRO GLU ASP LEU GLN SEQRES 12 A 146 LYS ILE GLN SEQRES 1 B 146 MET ALA GLN GLU ARG PRO SER CYS ALA VAL GLU PRO GLU SEQRES 2 B 146 HIS VAL GLN ARG LEU LEU LEU SER SER ARG GLU ALA LYS SEQRES 3 B 146 LYS SER ALA TYR CYS PRO TYR SER ARG PHE PRO VAL GLY SEQRES 4 B 146 ALA ALA LEU LEU THR GLY ASP GLY ARG ILE PHE SER GLY SEQRES 5 B 146 CYS ASN ILE GLU ASN ALA CYS TYR PRO LEU GLY VAL CYS SEQRES 6 B 146 ALA GLU ARG THR ALA ILE GLN LYS ALA ILE SER GLU GLY SEQRES 7 B 146 TYR LYS ASP PHE ARG ALA ILE ALA ILE SER SER ASP LEU SEQRES 8 B 146 GLN GLU GLU PHE ILE SER PRO CYS GLY ALA CYS ARG GLN SEQRES 9 B 146 VAL MET ARG GLU PHE GLY THR ASP TRP ALA VAL TYR MET SEQRES 10 B 146 THR LYS PRO ASP GLY THR PHE VAL VAL ARG THR VAL GLN SEQRES 11 B 146 GLU LEU LEU PRO ALA SER PHE GLY PRO GLU ASP LEU GLN SEQRES 12 B 146 LYS ILE GLN SEQRES 1 C 146 MET ALA GLN GLU ARG PRO SER CYS ALA VAL GLU PRO GLU SEQRES 2 C 146 HIS VAL GLN ARG LEU LEU LEU SER SER ARG GLU ALA LYS SEQRES 3 C 146 LYS SER ALA TYR CYS PRO TYR SER ARG PHE PRO VAL GLY SEQRES 4 C 146 ALA ALA LEU LEU THR GLY ASP GLY ARG ILE PHE SER GLY SEQRES 5 C 146 CYS ASN ILE GLU ASN ALA CYS TYR PRO LEU GLY VAL CYS SEQRES 6 C 146 ALA GLU ARG THR ALA ILE GLN LYS ALA ILE SER GLU GLY SEQRES 7 C 146 TYR LYS ASP PHE ARG ALA ILE ALA ILE SER SER ASP LEU SEQRES 8 C 146 GLN GLU GLU PHE ILE SER PRO CYS GLY ALA CYS ARG GLN SEQRES 9 C 146 VAL MET ARG GLU PHE GLY THR ASP TRP ALA VAL TYR MET SEQRES 10 C 146 THR LYS PRO ASP GLY THR PHE VAL VAL ARG THR VAL GLN SEQRES 11 C 146 GLU LEU LEU PRO ALA SER PHE GLY PRO GLU ASP LEU GLN SEQRES 12 C 146 LYS ILE GLN SEQRES 1 D 146 MET ALA GLN GLU ARG PRO SER CYS ALA VAL GLU PRO GLU SEQRES 2 D 146 HIS VAL GLN ARG LEU LEU LEU SER SER ARG GLU ALA LYS SEQRES 3 D 146 LYS SER ALA TYR CYS PRO TYR SER ARG PHE PRO VAL GLY SEQRES 4 D 146 ALA ALA LEU LEU THR GLY ASP GLY ARG ILE PHE SER GLY SEQRES 5 D 146 CYS ASN ILE GLU ASN ALA CYS TYR PRO LEU GLY VAL CYS SEQRES 6 D 146 ALA GLU ARG THR ALA ILE GLN LYS ALA ILE SER GLU GLY SEQRES 7 D 146 TYR LYS ASP PHE ARG ALA ILE ALA ILE SER SER ASP LEU SEQRES 8 D 146 GLN GLU GLU PHE ILE SER PRO CYS GLY ALA CYS ARG GLN SEQRES 9 D 146 VAL MET ARG GLU PHE GLY THR ASP TRP ALA VAL TYR MET SEQRES 10 D 146 THR LYS PRO ASP GLY THR PHE VAL VAL ARG THR VAL GLN SEQRES 11 D 146 GLU LEU LEU PRO ALA SER PHE GLY PRO GLU ASP LEU GLN SEQRES 12 D 146 LYS ILE GLN HET ZN A 147 1 HET SO4 A1005 5 HET URD A1001 17 HET ZN B 147 1 HET URD B1002 17 HET ZN C 147 1 HET URD C1003 17 HET ZN D 147 1 HET URD D1004 17 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM URD 1-((2R,3R,4S,5R)-TETRAHYDRO-3,4-DIHYDROXY-5- HETNAM 2 URD (HYDROXYMETHYL)FURAN-2-YL)PYRIDINE-2,4(1H,3H)-DIONE HETSYN URD 3-DEAZAURIDINE FORMUL 5 ZN 4(ZN 2+) FORMUL 6 SO4 O4 S 2- FORMUL 7 URD 4(C10 H13 N O6) FORMUL 14 HOH *309(H2 O) HELIX 1 1 PRO A 12 ALA A 29 1 18 HELIX 2 2 CYS A 59 GLY A 63 5 5 HELIX 3 3 CYS A 65 GLU A 77 1 13 HELIX 4 4 CYS A 99 PHE A 109 1 11 HELIX 5 5 VAL A 129 LEU A 133 1 5 HELIX 6 6 GLY A 138 GLN A 143 5 6 HELIX 7 7 GLU B 11 ALA B 29 1 19 HELIX 8 8 CYS B 59 GLY B 63 5 5 HELIX 9 9 CYS B 65 GLU B 77 1 13 HELIX 10 10 CYS B 99 PHE B 109 1 11 HELIX 11 11 VAL B 129 LEU B 133 1 5 HELIX 12 12 GLY B 138 GLN B 143 5 6 HELIX 13 13 GLU C 11 ALA C 29 1 19 HELIX 14 14 CYS C 59 GLY C 63 5 5 HELIX 15 15 CYS C 65 GLU C 77 1 13 HELIX 16 16 CYS C 99 PHE C 109 1 11 HELIX 17 17 VAL C 129 LEU C 133 1 5 HELIX 18 18 GLY C 138 GLN C 143 5 6 HELIX 19 19 PRO D 12 ALA D 29 1 18 HELIX 20 20 CYS D 59 GLY D 63 5 5 HELIX 21 21 CYS D 65 GLU D 77 1 13 HELIX 22 22 CYS D 99 PHE D 109 1 11 HELIX 23 23 VAL D 129 LEU D 133 1 5 HELIX 24 24 GLY D 138 GLN D 143 5 6 SHEET 1 A 5 ILE A 49 CYS A 53 0 SHEET 2 A 5 VAL A 38 THR A 44 -1 N LEU A 42 O PHE A 50 SHEET 3 A 5 PHE A 82 SER A 89 -1 O ALA A 84 N LEU A 43 SHEET 4 A 5 ALA A 114 THR A 118 1 O TYR A 116 N ILE A 85 SHEET 5 A 5 PHE A 124 THR A 128 -1 O VAL A 125 N MET A 117 SHEET 1 B 5 ILE B 49 CYS B 53 0 SHEET 2 B 5 VAL B 38 THR B 44 -1 N LEU B 42 O PHE B 50 SHEET 3 B 5 PHE B 82 SER B 89 -1 O SER B 88 N GLY B 39 SHEET 4 B 5 ALA B 114 THR B 118 1 O TYR B 116 N ILE B 85 SHEET 5 B 5 PHE B 124 THR B 128 -1 O VAL B 125 N MET B 117 SHEET 1 C 5 ILE C 49 CYS C 53 0 SHEET 2 C 5 VAL C 38 THR C 44 -1 N ALA C 40 O GLY C 52 SHEET 3 C 5 PHE C 82 SER C 89 -1 O ARG C 83 N LEU C 43 SHEET 4 C 5 ALA C 114 THR C 118 1 O TYR C 116 N ILE C 85 SHEET 5 C 5 PHE C 124 THR C 128 -1 O VAL C 125 N MET C 117 SHEET 1 D 5 ILE D 49 CYS D 53 0 SHEET 2 D 5 VAL D 38 THR D 44 -1 N LEU D 42 O PHE D 50 SHEET 3 D 5 PHE D 82 SER D 89 -1 O ARG D 83 N LEU D 43 SHEET 4 D 5 ALA D 114 THR D 118 1 O TYR D 116 N ILE D 85 SHEET 5 D 5 PHE D 124 THR D 128 -1 O VAL D 125 N MET D 117 LINK SG CYS A 65 ZN ZN A 147 1555 1555 2.44 LINK SG CYS A 99 ZN ZN A 147 1555 1555 2.34 LINK SG CYS A 102 ZN ZN A 147 1555 1555 2.35 LINK ZN ZN A 147 O HOH A1006 1555 1555 2.12 LINK SG CYS B 65 ZN ZN B 147 1555 1555 2.41 LINK SG CYS B 99 ZN ZN B 147 1555 1555 2.40 LINK SG CYS B 102 ZN ZN B 147 1555 1555 2.34 LINK ZN ZN B 147 O HOH B1003 1555 1555 2.20 LINK SG CYS C 65 ZN ZN C 147 1555 1555 2.31 LINK SG CYS C 99 ZN ZN C 147 1555 1555 2.40 LINK SG CYS C 102 ZN ZN C 147 1555 1555 2.37 LINK ZN ZN C 147 O HOH C1004 1555 1555 2.15 LINK SG CYS D 65 ZN ZN D 147 1555 1555 2.45 LINK SG CYS D 99 ZN ZN D 147 1555 1555 2.45 LINK SG CYS D 102 ZN ZN D 147 1555 1555 2.34 LINK ZN ZN D 147 O HOH D1005 1555 1555 2.22 SITE 1 AC1 4 CYS A 65 CYS A 99 CYS A 102 HOH A1006 SITE 1 AC2 4 CYS B 65 CYS B 99 CYS B 102 HOH B1003 SITE 1 AC3 4 CYS C 65 CYS C 99 CYS C 102 HOH C1004 SITE 1 AC4 4 CYS D 65 CYS D 99 CYS D 102 HOH D1005 SITE 1 AC5 4 GLN A 130 ALA A 135 HOH A1010 HOH A1070 SITE 1 AC6 15 PHE A 36 VAL A 38 ASN A 54 GLU A 56 SITE 2 AC6 15 CYS A 65 ALA A 66 GLU A 67 ILE A 96 SITE 3 AC6 15 SER A 97 PRO A 98 HOH A1007 ALA C 58 SITE 4 AC6 15 CYS C 59 TYR C 60 PRO C 61 SITE 1 AC7 15 PHE A 137 PHE B 36 VAL B 38 ASN B 54 SITE 2 AC7 15 GLU B 56 CYS B 65 ALA B 66 GLU B 67 SITE 3 AC7 15 SER B 97 HOH B1003 HOH B1004 ALA D 58 SITE 4 AC7 15 CYS D 59 TYR D 60 PRO D 61 SITE 1 AC8 15 ALA A 58 CYS A 59 TYR A 60 PRO A 61 SITE 2 AC8 15 PHE C 36 VAL C 38 ASN C 54 GLU C 56 SITE 3 AC8 15 VAL C 64 CYS C 65 ALA C 66 GLU C 67 SITE 4 AC8 15 SER C 97 PRO C 98 HOH C1005 SITE 1 AC9 15 ALA B 58 CYS B 59 TYR B 60 PRO B 61 SITE 2 AC9 15 PHE D 36 VAL D 38 ASN D 54 GLU D 56 SITE 3 AC9 15 CYS D 65 ALA D 66 GLU D 67 SER D 97 SITE 4 AC9 15 PRO D 98 HOH D1005 HOH D1006 CRYST1 82.237 92.361 180.531 90.00 90.00 90.00 I 2 2 2 32 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 0.012160 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005539 0.00000