PDB Short entry for 2JAW HEADER HYDROLASE 30-NOV-06 2JAW TITLE CRYSTAL STRUCTURE OF D41N VARIANT OF HUMAN MITOCHONDRIAL 5'(3')- TITLE 2 DEOXYRIBONUCLEOTIDASE (MDN) IN COMPLEX WITH 5-BROMOVINYLDEOXYURIDINE TITLE 3 5'-MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'(3')-DEOXYRIBONUCLEOTIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 32-228; COMPND 5 SYNONYM: 5', 3'-NUCLEOTIDASE, MITOCHONDRIAL, MITOCHONDRIAL COMPND 6 DEOXYRIBONUCLEOTIDASE, DEOXY-5'-NUCLEOTIDASE 2 , DNT-2; COMPND 7 EC: 3.1.3.-; COMPND 8 ENGINEERED: YES; COMPND 9 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET20B KEYWDS TRANSIT PEPTIDE, NUCLEOTIDE-BINDING, MITOCHONDRIAL, METAL-BINDING, KEYWDS 2 ALFA BETA FOLD, NUCLEOTIDE- BINDING, NUCLEOTIDE METABOLISM, KEYWDS 3 HYDROLASE, MAGNESIUM, MITOCHONDRION EXPDTA X-RAY DIFFRACTION AUTHOR K.WALLDEN,B.RUZZENENTE,V.BIANCHI,P.NORDLUND REVDAT 7 24-JUL-19 2JAW 1 REMARK REVDAT 6 10-JUL-19 2JAW 1 REMARK REVDAT 5 06-FEB-19 2JAW 1 REMARK REVDAT 4 30-JAN-19 2JAW 1 REMARK REVDAT 3 24-FEB-09 2JAW 1 VERSN REVDAT 2 29-APR-08 2JAW 1 JRNL REMARK REVDAT 1 20-NOV-07 2JAW 0 JRNL AUTH K.WALLDEN,A.RINALDO-MATTHIS,B.RUZZENENTE,C.RAMPAZZO, JRNL AUTH 2 V.BIANCHI,P.NORDLUND JRNL TITL CRYSTAL STRUCTURES OF HUMAN AND MURINE JRNL TITL 2 DEOXYRIBONUCLEOTIDASES: INSIGHTS INTO RECOGNITION OF JRNL TITL 3 SUBSTRATES AND NUCLEOTIDE ANALOGUES. JRNL REF BIOCHEMISTRY V. 46 13809 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17985935 JRNL DOI 10.1021/BI7014794 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 2079 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1122 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1510 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1599 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : 0.46000 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): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.717 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1676 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2278 ; 1.426 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 193 ; 5.938 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;29.496 ;22.892 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 275 ;13.899 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;20.664 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 237 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1299 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 752 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1142 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 151 ; 0.158 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 37 ; 0.189 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.126 ; 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): 1000 ; 0.880 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1580 ; 1.530 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 782 ; 2.440 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 698 ; 3.903 ; 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 2JAW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1290030686. 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) : 0.81150 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21939 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.800 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG8000, 0.050 M POTASSIUM REMARK 280 DIHYDROGEN PHOSPHATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 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 53.18700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.80200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.80200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.78050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.80200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.80200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.59350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.80200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.80200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.78050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.80200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.80200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.59350 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 53.18700 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.7 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 BIOMT1 2 0.000000 -1.000000 0.000000 73.60400 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 73.60400 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.18700 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 41 TO ASN 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 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 CYS A 228 CA C O CB SG 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 OE1 GLU A 106 O HOH A 2063 2.12 REMARK 500 O HOH A 2141 O HOH A 2144 2.13 REMARK 500 O HOH A 2086 O HOH A 2087 2.19 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 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -4.1 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 -72.12 -96.27 REMARK 500 VAL A 45 -51.04 -130.93 REMARK 500 ASN A 100 -1.26 71.32 REMARK 500 SER A 213 172.67 179.74 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 A1229 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 119 O REMARK 620 2 THR A 124 O 102.9 REMARK 620 3 HOH A2078 O 168.0 79.2 REMARK 620 4 LEU A 121 O 107.2 100.9 83.8 REMARK 620 5 HOH A2075 O 87.5 157.6 86.8 94.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1230 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2167 O REMARK 620 2 ASP A 176 OD1 87.2 REMARK 620 3 HOH A2168 O 97.0 82.8 REMARK 620 4 ASP A 43 O 84.1 90.8 173.5 REMARK 620 5 BVP A1228 O2P 84.0 157.1 77.3 109.3 REMARK 620 6 BVP A1228 O1P 88.4 175.6 98.3 88.1 22.2 REMARK 620 7 ASN A 41 OD1 176.5 91.3 85.9 92.7 98.5 93.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BVP A1228 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1229 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1230 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MH9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF DEOXYRIBONUCLEOTIDASE REMARK 900 RELATED ID: 1Q91 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIALDEOXYRIBONUCLEOTIDASE IN REMARK 900 COMPLEX WITH THE INHIBITOR DPB-T REMARK 900 RELATED ID: 1Q92 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIALDEOXYRIBONUCLEOTIDASE IN REMARK 900 COMPLEX WITH THE INHIBITOR PMCP-U REMARK 900 RELATED ID: 1Z4I RELATED DB: PDB REMARK 900 STRUCTURE OF THE D41N VARIANT OF THE HUMAN REMARK 900 MITOCHONDRIALDEOXYRIBONUCLEOTIDASE IN COMPLEX WITH DEOXYRIBOURIDINE REMARK 900 5'-MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4J RELATED DB: PDB REMARK 900 STRUCTURE OF THE D41N VARIANT OF THE HUMAN REMARK 900 MITOCHONDRIALDEOXYRIBONUCLEOTIDASE IN COMPLEX WITH URIDINE 2'- REMARK 900 MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4K RELATED DB: PDB REMARK 900 STRUCTURE OF THE D41N VARIANT OF THE HUMAN REMARK 900 MITOCHONDRIALDEOXYRIBONUCLEOTIDASE IN COMPLEX WITH THYMIDINE 3'- REMARK 900 MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4L RELATED DB: PDB REMARK 900 STRUCTURE OF THE D41N VARIANT OF THE HUMAN REMARK 900 MITOCHONDRIALDEOXYRIBONUCLEOTIDASE IN COMPLEX WITH THYMIDINE 5'- REMARK 900 MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4M RELATED DB: PDB REMARK 900 STRUCTURE OF THE D41N VARIANT OF THE HUMAN REMARK 900 MITOCHONDRIALDEOXYRIBONUCLEOTIDASE IN COMPLEX WITH URIDINE 5'- REMARK 900 MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4P RELATED DB: PDB REMARK 900 STRUCTURE OF THE D41N VARIANT OF THE HUMAN REMARK 900 MITOCHONDRIALDEOXYRIBONUCLEOTIDASE IN COMPLEX WITH REMARK 900 DEOXYRIBOGUANOSINE5'-MONOPHOSPHATE REMARK 900 RELATED ID: 1Z4Q RELATED DB: PDB REMARK 900 STRUCTURE OF THE D41N VARIANT OF THE HUMAN REMARK 900 MITOCHONDRIALDEOXYRIBONUCLEOTIDASE IN COMPLEX WITH 2',3'-DIDEOXY-2', REMARK 900 3-DIDEHYDROTHYMIDINE 5'-MONOPHOSPHATE (D4T-MP) REMARK 900 RELATED ID: 2JAU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D41N VARIANT OF HUMAN MITOCHONDRIAL 5'(3')- REMARK 900 DEOXYRIBONUCLEOTIDASE (MDN ) IN COMPLEX WITH 3'-AZIDOTHYMIDINE 5'- REMARK 900 MONOPHOSPHATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 MIRLGGWCARRLCSAAVPAGRRGAAGGLGLAGGRALRVLVDMDGVLADFEGGFLRKFRAR REMARK 999 FPDQPFIA DBREF 2JAW A 32 228 UNP Q9NPB1 NT5M_HUMAN 32 228 SEQADV 2JAW 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 BVP A1228 28 HET MG A1229 1 HET MG A1230 1 HETNAM BVP (E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN BVP BVDU-MP FORMUL 2 BVP C11 H14 BR N2 O8 P FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *172(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 217 ARG A 226 1 10 SHEET 1 AA 6 ILE A 159 LEU A 161 0 SHEET 2 AA 6 THR A 124 THR A 130 1 O ILE A 128 N VAL A 160 SHEET 3 AA 6 LEU A 36 VAL A 40 1 O LEU A 36 N ASP A 125 SHEET 4 AA 6 LEU A 172 ASP A 175 1 O LEU A 172 N LEU A 39 SHEET 5 AA 6 GLU A 190 PHE A 194 1 O GLU A 190 N LEU A 173 SHEET 6 AA 6 ARG A 209 LEU A 211 1 O ARG A 209 N LEU A 193 LINK MG MG A1229 O ALA A 119 1555 1555 2.36 LINK MG MG A1229 O THR A 124 1555 1555 2.34 LINK MG MG A1229 O HOH A2078 1555 1555 2.47 LINK MG MG A1229 O LEU A 121 1555 1555 2.41 LINK MG MG A1229 O HOH A2075 1555 1555 2.26 LINK MG MG A1230 O HOH A2167 1555 1555 2.12 LINK MG MG A1230 OD1 ASP A 176 1555 1555 2.13 LINK MG MG A1230 O HOH A2168 1555 1555 2.15 LINK MG MG A1230 O ASP A 43 1555 1555 2.01 LINK MG MG A1230 O2PABVP A1228 1555 1555 1.92 LINK MG MG A1230 O1PBBVP A1228 1555 1555 2.13 LINK MG MG A1230 OD1 ASN A 41 1555 1555 2.01 SITE 1 AC1 21 ASN A 41 MET A 42 ASP A 43 PHE A 49 SITE 2 AC1 21 TRP A 76 VAL A 77 SER A 78 TRP A 96 SITE 3 AC1 21 THR A 130 SER A 131 PRO A 132 ILE A 133 SITE 4 AC1 21 LYS A 143 LYS A 165 MG A1230 HOH A2167 SITE 5 AC1 21 HOH A2168 HOH A2169 HOH A2170 HOH A2171 SITE 6 AC1 21 HOH A2172 SITE 1 AC2 6 ALA A 119 LEU A 121 THR A 124 HOH A2075 SITE 2 AC2 6 HOH A2078 HOH A2079 SITE 1 AC3 6 ASN A 41 ASP A 43 ASP A 176 BVP A1228 SITE 2 AC3 6 HOH A2167 HOH A2168 CRYST1 73.604 73.604 106.374 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 0.013586 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009401 0.00000