HEADER HYDROLASE 29-NOV-06 2JAO TITLE CRYSTAL STRUCTURE OF D12N VARIANT OF MOUSE CYTOSOLIC 5'(3')- TITLE 2 DEOXYRIBONUCLEOTIDASE (CDN) IN COMPLEX WITH DEOXYGUANOSINE 5'- TITLE 3 MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'(3')-DEOXYRIBONUCLEOTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOSOLIC TYPE, CYTOSOLIC 5', 3'-PYRIMIDINE NUCLEOTIDASE, COMPND 5 DEOXY-5'-NUCLEOTIDASE 1, DNT-1, CYTOSOLIC DEOXYRIBONUCLEOTIDASE; COMPND 6 EC: 3.1.3.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; 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 NUCLEOTIDE METABOLISM, NUCLEOTIDE-BINDING, ALPHA-BETA FOLD, METAL- KEYWDS 2 BINDING, HYDROLASE, MAGNESIUM, CYTOSOL EXPDTA X-RAY DIFFRACTION AUTHOR K.WALLDEN,B.RUZZENENTE,V.BIANCHI,P.NORDLUND REVDAT 7 08-MAY-24 2JAO 1 REMARK LINK REVDAT 6 15-MAY-19 2JAO 1 REMARK REVDAT 5 17-JAN-18 2JAO 1 REMARK REVDAT 4 23-MAR-10 2JAO 1 VERSN REVDAT 3 24-FEB-09 2JAO 1 VERSN REVDAT 2 29-APR-08 2JAO 1 JRNL REMARK REVDAT 1 20-NOV-07 2JAO 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0032 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18178 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 985 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1352 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1940 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1595 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.139 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.133 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.224 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1717 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2344 ; 1.560 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 210 ; 5.970 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 89 ;33.909 ;23.483 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 297 ;14.635 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.415 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 253 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1327 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 623 ; 0.192 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1114 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 130 ; 0.175 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.042 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 28 ; 0.220 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.196 ; 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): 1055 ; 1.129 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1638 ; 1.667 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 786 ; 2.414 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 698 ; 3.818 ; 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 2JAO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1290030673. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1410 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19090 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.910 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 (%): 61.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 0.1 M BIS REMARK 280 -TRIS PH 5.5, 23-25% PEG3350 AT 6 DEGREES CELSIUS, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 279K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.17333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.58667 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.17333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.58667 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.4 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 -1.000000 0.000000 0.000000 -38.12500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -66.03444 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 12 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 VAL A 3 REMARK 465 LEU A 200 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 NH1 ARG A 30 O HOH A 2023 2.09 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 ARG A 5 137.46 -34.88 REMARK 500 MET A 13 -73.40 -95.61 REMARK 500 VAL A 16 -50.59 -129.68 REMARK 500 LEU A 122 -55.65 -120.43 REMARK 500 SER A 184 -178.87 -175.18 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 A1202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 12 OD1 REMARK 620 2 ASP A 14 O 86.0 REMARK 620 3 ASP A 147 OD1 89.1 81.6 REMARK 620 4 DGP A1201 OP3 99.9 113.4 162.8 REMARK 620 5 DGP A1201 OP3 92.5 91.5 172.8 22.9 REMARK 620 6 HOH A2174 O 92.9 169.4 87.9 77.2 99.1 REMARK 620 7 HOH A2175 O 173.9 88.2 88.1 84.1 89.6 92.5 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 GOL A 1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGP A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JAR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D12N VARIANT OF MOUSE CYTOSOLIC 5'(3')- REMARK 900 DEOXYRIBONUCLEOTIDASE (CDN) IN COMPLEX WITH DEOXYURIDINE 5'- REMARK 900 MONOPHOSPHATE DBREF 2JAO A 1 200 UNP Q9JM14 NT5C_MOUSE 1 200 SEQADV 2JAO ASN A 12 UNP Q9JM14 ASP 12 ENGINEERED MUTATION SEQRES 1 A 200 MET ALA VAL LYS ARG PRO VAL ARG VAL LEU VAL ASN MET SEQRES 2 A 200 ASP GLY VAL LEU ALA ASP PHE GLU SER GLY LEU LEU GLN SEQRES 3 A 200 GLY PHE ARG ARG ARG PHE PRO GLU GLU PRO HIS VAL PRO SEQRES 4 A 200 LEU GLU GLN ARG ARG GLY PHE LEU ALA ASN GLU GLN TYR SEQRES 5 A 200 GLY ALA LEU ARG PRO ASP LEU ALA GLU LYS VAL ALA SER SEQRES 6 A 200 VAL TYR GLU SER PRO GLY PHE PHE LEU ASN LEU GLU PRO SEQRES 7 A 200 ILE PRO GLY ALA LEU ASP ALA LEU ARG GLU MET ASN ASP SEQRES 8 A 200 MET LYS ASP THR GLU VAL PHE ILE CYS THR THR PRO LEU SEQRES 9 A 200 LEU LYS TYR ASP HIS CYS VAL GLY GLU LYS TYR ARG TRP SEQRES 10 A 200 VAL GLU GLN ASN LEU GLY PRO GLU PHE VAL GLU ARG ILE SEQRES 11 A 200 ILE LEU THR ARG ASP LYS THR VAL VAL MET GLY ASP LEU SEQRES 12 A 200 LEU ILE ASP ASP LYS ASP ASN ILE GLN GLY LEU GLU GLU SEQRES 13 A 200 THR PRO SER TRP GLU HIS ILE LEU PHE THR CYS CYS HIS SEQRES 14 A 200 ASN GLN HIS LEU ALA LEU PRO PRO THR ARG ARG ARG LEU SEQRES 15 A 200 LEU SER TRP SER ASP ASN TRP ARG GLY ILE ILE GLU SER SEQRES 16 A 200 LYS ARG ALA SER LEU HET GOL A1200 6 HET DGP A1201 28 HET MG A1202 1 HETNAM GOL GLYCEROL HETNAM DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 DGP C10 H14 N5 O7 P FORMUL 4 MG MG 2+ FORMUL 5 HOH *175(H2 O) HELIX 1 1 ASP A 19 PHE A 32 1 14 HELIX 2 2 PRO A 39 ARG A 43 5 5 HELIX 3 3 LEU A 47 ARG A 56 1 10 HELIX 4 4 PRO A 57 GLU A 68 1 12 HELIX 5 5 GLY A 81 ASP A 91 1 11 HELIX 6 6 LYS A 106 HIS A 109 5 4 HELIX 7 7 CYS A 110 LEU A 122 1 13 HELIX 8 8 GLY A 123 GLU A 128 1 6 HELIX 9 9 ASP A 135 VAL A 139 5 5 HELIX 10 10 CYS A 167 GLN A 171 5 5 HELIX 11 11 ASN A 188 ALA A 198 1 11 SHEET 1 AA 6 ILE A 130 LEU A 132 0 SHEET 2 AA 6 THR A 95 THR A 101 1 O ILE A 99 N ILE A 131 SHEET 3 AA 6 VAL A 7 ASN A 12 1 O VAL A 7 N GLU A 96 SHEET 4 AA 6 LEU A 143 ASP A 146 1 O LEU A 143 N LEU A 10 SHEET 5 AA 6 GLU A 161 PHE A 165 1 O GLU A 161 N LEU A 144 SHEET 6 AA 6 ARG A 181 LEU A 182 1 N LEU A 182 O LEU A 164 LINK OD1 ASN A 12 MG MG A1202 1555 1555 2.16 LINK O ASP A 14 MG MG A1202 1555 1555 2.21 LINK OD1 ASP A 147 MG MG A1202 1555 1555 2.20 LINK OP3ADGP A1201 MG MG A1202 1555 1555 1.95 LINK OP3BDGP A1201 MG MG A1202 1555 1555 2.19 LINK MG MG A1202 O HOH A2174 1555 1555 2.08 LINK MG MG A1202 O HOH A2175 1555 1555 2.19 SITE 1 AC1 4 ARG A 5 LYS A 196 ARG A 197 SER A 199 SITE 1 AC2 20 ASN A 12 MET A 13 ASP A 14 PHE A 20 SITE 2 AC2 20 LEU A 47 ALA A 48 ASN A 49 TYR A 67 SITE 3 AC2 20 THR A 101 THR A 102 PRO A 103 LEU A 104 SITE 4 AC2 20 LYS A 114 LYS A 136 MG A1202 HOH A2171 SITE 5 AC2 20 HOH A2172 HOH A2173 HOH A2174 HOH A2175 SITE 1 AC3 6 ASN A 12 ASP A 14 ASP A 147 DGP A1201 SITE 2 AC3 6 HOH A2174 HOH A2175 CRYST1 76.250 76.250 85.760 90.00 90.00 120.00 P 62 6 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 0.013115 0.007572 0.000000 0.00000 SCALE2 0.000000 0.015144 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011660 0.00000