PDB Short entry for 1Z4J HEADER HYDROLASE 16-MAR-05 1Z4J TITLE STRUCTURE OF THE D41N VARIANT OF THE HUMAN MITOCHONDRIAL TITLE 2 DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH URIDINE 2'-MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'(3')-DEOXYRIBONUCLEOTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE, 5',3'-NUCLEOTIDASE, COMPND 5 MITOCHONDRIAL, DEOXY-5'-NUCLEOTIDASE 2, DNT-2; COMPND 6 EC: 3.1.3.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLYSS KEYWDS ALFA BETA FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.WALLDEN,B.RUZZENENTE,A.RINALDO-MATTHIS,V.BIANCHI,P.NORDLUND REVDAT 4 10-NOV-21 1Z4J 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1Z4J 1 VERSN REVDAT 2 24-FEB-09 1Z4J 1 VERSN REVDAT 1 26-JUL-05 1Z4J 0 JRNL AUTH K.WALLDEN,B.RUZZENENTE,A.RINALDO-MATTHIS,V.BIANCHI, JRNL AUTH 2 P.NORDLUND JRNL TITL STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY OF THE HUMAN JRNL TITL 2 MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE JRNL REF STRUCTURE V. 13 1081 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 16004879 JRNL DOI 10.1016/J.STR.2005.04.023 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 25876 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1369 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1881 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1970 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.2370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1597 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.35000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : 0.70000 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): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.873 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1672 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1488 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2270 ; 1.614 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3454 ; 0.904 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 193 ; 6.312 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 238 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1827 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 368 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 315 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1695 ; 0.249 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 941 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 101 ; 0.094 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.074 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 5 ; 0.257 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 54 ; 0.351 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.116 ; 0.200 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): 973 ; 1.026 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1577 ; 1.839 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 699 ; 2.787 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 693 ; 4.365 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 1Z4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032288. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27294 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, POTASSIUM DIHYDROGEN REMARK 280 PHOSPHATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 53.04250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.72650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.72650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.56375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.72650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.72650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.52125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.72650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.72650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.56375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.72650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.72650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.52125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.04250 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: DIMERIC 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 BIOMT1 2 0.000000 -1.000000 0.000000 73.45300 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 73.45300 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.04250 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 32 REMARK 465 GLY A 33 REMARK 465 CYS A 228 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 PRO A 227 O 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 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ASP A 63 CB - CG - OD2 ANGL. DEV. = 6.2 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 MET A 42 -72.76 -91.27 REMARK 500 VAL A 45 -52.70 -134.59 REMARK 500 ASN A 100 -0.55 73.50 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 MG A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 41 OD1 REMARK 620 2 ASP A 43 O 89.4 REMARK 620 3 ASP A 176 OD1 87.3 92.2 REMARK 620 4 U2P A3001 O2P 91.6 97.0 170.7 REMARK 620 5 HOH A4004 O 177.5 88.9 90.9 90.4 REMARK 620 6 HOH A4008 O 85.7 174.8 85.8 85.0 96.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A2001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 119 O REMARK 620 2 LEU A 121 O 104.0 REMARK 620 3 THR A 124 O 102.5 99.6 REMARK 620 4 HOH A4146 O 86.2 94.5 161.0 REMARK 620 5 HOH A4147 O 88.0 167.4 73.5 90.1 REMARK 620 6 HOH A4149 O 172.1 81.7 81.6 87.9 86.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U2P A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 4001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z4I RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH DEOXYRIBOURIDINE 5'-MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4K RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH THYMIDINE 3'-MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4L RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH THYMIDINE 5'-MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4M RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH URIDINE 5'-MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4P RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH DEOXYRIBOGUANOSINE 5'-MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4Q RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH 3'-DEOXY 2'3'-DIDEHYDROTHYMIDINE 5'- REMARK 900 MONOPHOSPHATE (D4T-MP) DBREF 1Z4J A 32 228 UNP Q9NPB1 NT5M_HUMAN 32 228 SEQADV 1Z4J ASN A 41 UNP Q9NPB1 ASP 41 ENGINEERED MUTATION SEQRES 1 A 197 GLY GLY ARG ALA LEU ARG VAL LEU VAL ASN MET ASP GLY SEQRES 2 A 197 VAL LEU ALA ASP PHE GLU GLY GLY PHE LEU ARG LYS PHE SEQRES 3 A 197 ARG ALA ARG PHE PRO ASP GLN PRO PHE ILE ALA LEU GLU SEQRES 4 A 197 ASP ARG ARG GLY PHE TRP VAL SER GLU GLN TYR GLY ARG SEQRES 5 A 197 LEU ARG PRO GLY LEU SER GLU LYS ALA ILE SER ILE TRP SEQRES 6 A 197 GLU SER LYS ASN PHE PHE PHE GLU LEU GLU PRO LEU PRO SEQRES 7 A 197 GLY ALA VAL GLU ALA VAL LYS GLU MET ALA SER LEU GLN SEQRES 8 A 197 ASN THR ASP VAL PHE ILE CYS THR SER PRO ILE LYS MET SEQRES 9 A 197 PHE LYS TYR CYS PRO TYR GLU LYS TYR ALA TRP VAL GLU SEQRES 10 A 197 LYS TYR PHE GLY PRO ASP PHE LEU GLU GLN ILE VAL LEU SEQRES 11 A 197 THR ARG ASP LYS THR VAL VAL SER ALA ASP LEU LEU ILE SEQRES 12 A 197 ASP ASP ARG PRO ASP ILE THR GLY ALA GLU PRO THR PRO SEQRES 13 A 197 SER TRP GLU HIS VAL LEU PHE THR ALA CYS HIS ASN GLN SEQRES 14 A 197 HIS LEU GLN LEU GLN PRO PRO ARG ARG ARG LEU HIS SER SEQRES 15 A 197 TRP ALA ASP ASP TRP LYS ALA ILE LEU ASP SER LYS ARG SEQRES 16 A 197 PRO CYS HET MG A1001 1 HET MG A2001 1 HET U2P A3001 21 HET GOL A4001 6 HETNAM MG MAGNESIUM ION HETNAM U2P PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H- HETNAM 2 U2P PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO- HETNAM 3 U2P FURAN-3-YL] ESTER HETNAM GOL GLYCEROL HETSYN U2P URIDINE-2'-PHOSPHATE; 2'-URIDINEMONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG 2(MG 2+) FORMUL 4 U2P C9 H13 N2 O9 P FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *157(H2 O) HELIX 1 1 ASP A 48 PHE A 61 1 14 HELIX 2 2 ALA A 68 ARG A 72 5 5 HELIX 3 3 TRP A 76 ARG A 85 1 10 HELIX 4 4 GLY A 87 GLU A 97 1 11 HELIX 5 5 GLY A 110 LEU A 121 1 12 HELIX 6 6 TYR A 138 GLY A 152 1 15 HELIX 7 7 PRO A 153 GLU A 157 5 5 HELIX 8 8 ASP A 164 VAL A 168 5 5 HELIX 9 9 ASP A 217 SER A 224 1 8 SHEET 1 A 6 ILE A 159 LEU A 161 0 SHEET 2 A 6 THR A 124 THR A 130 1 N ILE A 128 O VAL A 160 SHEET 3 A 6 LEU A 36 ASN A 41 1 N VAL A 40 O PHE A 127 SHEET 4 A 6 LEU A 172 ASP A 175 1 O LEU A 172 N LEU A 39 SHEET 5 A 6 GLU A 190 PHE A 194 1 O VAL A 192 N LEU A 173 SHEET 6 A 6 ARG A 209 LEU A 211 1 O ARG A 209 N LEU A 193 LINK OD1 ASN A 41 MG MG A1001 1555 1555 1.97 LINK O ASP A 43 MG MG A1001 1555 1555 1.86 LINK O ALA A 119 MG MG A2001 1555 1555 2.37 LINK O LEU A 121 MG MG A2001 1555 1555 2.49 LINK O THR A 124 MG MG A2001 1555 1555 2.37 LINK OD1 ASP A 176 MG MG A1001 1555 1555 1.97 LINK MG MG A1001 O2P U2P A3001 1555 1555 1.93 LINK MG MG A1001 O HOH A4004 1555 1555 1.91 LINK MG MG A1001 O HOH A4008 1555 1555 2.00 LINK MG MG A2001 O HOH A4146 1555 1555 2.38 LINK MG MG A2001 O HOH A4147 1555 1555 2.72 LINK MG MG A2001 O HOH A4149 1555 1555 2.53 SITE 1 AC1 6 ASN A 41 ASP A 43 ASP A 176 U2P A3001 SITE 2 AC1 6 HOH A4004 HOH A4008 SITE 1 AC2 6 ALA A 119 LEU A 121 THR A 124 HOH A4146 SITE 2 AC2 6 HOH A4147 HOH A4149 SITE 1 AC3 18 ASN A 41 ASP A 43 PHE A 49 TRP A 76 SITE 2 AC3 18 VAL A 77 THR A 130 SER A 131 PRO A 132 SITE 3 AC3 18 LYS A 143 LYS A 165 MG A1001 HOH A4004 SITE 4 AC3 18 HOH A4008 HOH A4011 HOH A4037 HOH A4039 SITE 5 AC3 18 HOH A4070 HOH A4144 SITE 1 AC4 5 GLU A 97 MET A 135 HIS A 212 HOH A4030 SITE 2 AC4 5 HOH A4093 CRYST1 73.453 73.453 106.085 90.00 90.00 90.00 P 43 21 2 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 0.013614 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009426 0.00000