HEADER DNA 05-JUN-17 5W1Z TITLE CRYSTAL STRUCTURE OF INOSINE-SUBSTITUTED DECAMER DUPLEX DNA (I4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS INOSINE, DNA CRYSTAL STRUCTURE, DEOXYINONSINE, CIRCULAR DICHROISM OF KEYWDS 2 MODIFIED DNA, DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.S.PALLAN,M.EGLI REVDAT 4 13-MAR-24 5W1Z 1 LINK REVDAT 3 24-OCT-18 5W1Z 1 JRNL REVDAT 2 13-SEP-17 5W1Z 1 JRNL REVDAT 1 30-AUG-17 5W1Z 0 JRNL AUTH J.P.PETERS,E.A.KOWAL,P.S.PALLAN,M.EGLI,L.J.MAHER 3RD. JRNL TITL COMPARATIVE ANALYSIS OF INOSINE-SUBSTITUTED DUPLEX DNA BY JRNL TITL 2 CIRCULAR DICHROISM AND X-RAY CRYSTALLOGRAPHY. JRNL REF J. BIOMOL. STRUCT. DYN. V. 36 2753 2018 JRNL REFN ESSN 1538-0254 JRNL PMID 28818035 JRNL DOI 10.1080/07391102.2017.1369164 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 12813 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 801 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) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 655 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3160 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 792 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.70000 REMARK 3 B22 (A**2) : -0.80000 REMARK 3 B33 (A**2) : -1.11000 REMARK 3 B12 (A**2) : 0.37000 REMARK 3 B13 (A**2) : 0.73000 REMARK 3 B23 (A**2) : -0.14000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.815 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 902 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 411 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1382 ; 2.085 ; 1.325 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1003 ; 1.680 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL 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): 123 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 445 ; 0.037 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 156 ; 0.007 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 902 ; 2.725 ; 1.956 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 901 ; 2.726 ; 1.956 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1383 ; 3.667 ; 2.961 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1243 ; 5.919 ;19.627 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1204 ; 5.825 ;18.918 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 10 REMARK 3 RESIDUE RANGE : B 11 B 20 REMARK 3 ORIGIN FOR THE GROUP (A): 18.3731 6.1238 12.9851 REMARK 3 T TENSOR REMARK 3 T11: 0.0230 T22: 0.0169 REMARK 3 T33: 0.0550 T12: -0.0107 REMARK 3 T13: -0.0247 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 0.2398 L22: 0.1301 REMARK 3 L33: 0.2130 L12: -0.1479 REMARK 3 L13: 0.2213 L23: -0.1531 REMARK 3 S TENSOR REMARK 3 S11: -0.0006 S12: 0.0276 S13: 0.0179 REMARK 3 S21: 0.0293 S22: -0.0336 S23: -0.0462 REMARK 3 S31: -0.0128 S32: 0.0286 S33: 0.0343 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 10 REMARK 3 RESIDUE RANGE : D 11 D 20 REMARK 3 ORIGIN FOR THE GROUP (A): 13.4929 21.9646 -4.5350 REMARK 3 T TENSOR REMARK 3 T11: 0.0092 T22: 0.0086 REMARK 3 T33: 0.0548 T12: -0.0027 REMARK 3 T13: -0.0144 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.3202 L22: 0.3837 REMARK 3 L33: 0.5802 L12: -0.1075 REMARK 3 L13: -0.2229 L23: -0.2789 REMARK 3 S TENSOR REMARK 3 S11: -0.0058 S12: 0.0351 S13: -0.0313 REMARK 3 S21: 0.0105 S22: -0.0519 S23: 0.0206 REMARK 3 S31: -0.0080 S32: 0.0168 S33: 0.0576 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: NULL REMARK 4 REMARK 4 5W1Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228296. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13618 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 32.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 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: SAD 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 (%): 38.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROPLETS (2 UL) CONTAINING REMARK 280 OLIGONUCLEOTIDE (0.6 MM), SODIUM CACODYLATE (20 MM, PH 6.0), REMARK 280 MAGNESIUM ACETATE (12.5 MM), AND MPD (20% V/V) THAT WERE REMARK 280 EQUILIBRATED AGAINST A 1 ML RESERVOIR OF SODIUM CACODYLATE (50 REMARK 280 MM, PH 6.5), MAGNESIUM ACETATE (25 MM), AND MPD (40% V/V), VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 279K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 DC C 6 O5' - P - OP1 ANGL. DEV. = -7.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DI A 9 0.07 SIDE CHAIN REMARK 500 DI B 19 0.06 SIDE CHAIN 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 NA A 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 6 O2 REMARK 620 2 DC B 16 O2 85.4 REMARK 620 3 DC B 17 O4' 140.5 65.8 REMARK 620 4 HOH B 127 O 100.8 113.7 69.8 REMARK 620 5 HOH B 128 O 106.0 94.6 103.0 142.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 203 O REMARK 620 2 HOH A 231 O 90.5 REMARK 620 3 HOH A 233 O 106.8 89.7 REMARK 620 4 HOH B 106 O 87.2 86.6 165.7 REMARK 620 5 HOH B 130 O 163.4 86.9 89.6 76.3 REMARK 620 6 HOH B 134 O 91.6 170.6 98.5 84.3 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 218 O REMARK 620 2 HOH B 123 O 119.4 REMARK 620 3 HOH D 214 O 86.6 85.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 224 O REMARK 620 2 HOH C 209 O 90.2 REMARK 620 3 HOH C 223 O 177.3 88.1 REMARK 620 4 HOH C 224 O 84.4 89.7 93.5 REMARK 620 5 HOH D 213 O 88.4 177.8 93.3 91.8 REMARK 620 6 HOH D 233 O 100.3 89.9 81.9 175.3 88.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 118 O REMARK 620 2 DC C 6 OP1 126.4 REMARK 620 3 HOH C 230 O 111.2 112.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 210 O REMARK 620 2 HOH C 227 O 93.1 REMARK 620 3 HOH C 233 O 101.4 86.3 REMARK 620 4 HOH D 228 O 86.4 176.5 97.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 221 O REMARK 620 2 BRU D 18 O2 97.7 REMARK 620 3 DI D 19 O4' 90.1 104.1 REMARK 620 4 HOH D 237 O 103.1 132.8 117.6 REMARK 620 N 1 2 3 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DC B 17 and BRU B REMARK 800 18 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide BRU B 18 and DI B REMARK 800 19 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DC C 7 and BRU C REMARK 800 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide BRU C 8 and DI C REMARK 800 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DC D 17 and BRU D REMARK 800 18 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide BRU D 18 and DI D REMARK 800 19 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5W20 RELATED DB: PDB DBREF 5W1Z A 1 10 PDB 5W1Z 5W1Z 1 10 DBREF 5W1Z B 11 20 PDB 5W1Z 5W1Z 11 20 DBREF 5W1Z C 1 10 PDB 5W1Z 5W1Z 1 10 DBREF 5W1Z D 11 20 PDB 5W1Z 5W1Z 11 20 SEQRES 1 A 10 DC DC DA DI DI DC DC BRU DI DI SEQRES 1 B 10 DC DC DA DI DI DC DC BRU DI DI SEQRES 1 C 10 DC DC DA DI DI DC DC BRU DI DI SEQRES 1 D 10 DC DC DA DI DI DC DC BRU DI DI HET BRU A 8 20 HET BRU B 18 20 HET BRU C 8 20 HET BRU D 18 20 HET MG A 101 1 HET NA A 102 1 HET MG C 101 1 HET NA C 102 1 HET MG D 101 1 HET NA D 102 1 HET NA D 103 1 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 1 BRU 4(C9 H12 BR N2 O8 P) FORMUL 5 MG 3(MG 2+) FORMUL 6 NA 4(NA 1+) FORMUL 12 HOH *156(H2 O) LINK O3' DC A 7 P BRU A 8 1555 1555 1.60 LINK O3' BRU A 8 P DI A 9 1555 1555 1.60 LINK O3' DC B 17 P BRU B 18 1555 1555 1.60 LINK O3' BRU B 18 P DI B 19 1555 1555 1.59 LINK O3' DC C 7 P BRU C 8 1555 1555 1.59 LINK O3' BRU C 8 P DI C 9 1555 1555 1.62 LINK O3' DC D 17 P BRU D 18 1555 1555 1.60 LINK O3' BRU D 18 P DI D 19 1555 1555 1.63 LINK O2 DC A 6 NA NA A 102 1555 1555 2.75 LINK MG MG A 101 O HOH A 203 1555 1555 1.86 LINK MG MG A 101 O HOH A 231 1555 1555 2.16 LINK MG MG A 101 O HOH A 233 1555 1555 2.04 LINK MG MG A 101 O HOH B 106 1555 1545 2.39 LINK MG MG A 101 O HOH B 130 1555 1545 2.16 LINK MG MG A 101 O HOH B 134 1555 1545 2.08 LINK NA NA A 102 O2 DC B 16 1555 1555 2.81 LINK NA NA A 102 O4' DC B 17 1555 1555 3.15 LINK NA NA A 102 O HOH B 127 1555 1555 2.84 LINK NA NA A 102 O HOH B 128 1555 1555 2.94 LINK O HOH A 218 NA NA D 102 1555 1555 2.69 LINK O HOH A 224 MG MG C 101 1464 1555 1.95 LINK O HOH B 118 NA NA C 102 1555 1555 2.56 LINK O HOH B 123 NA NA D 102 1555 1555 3.06 LINK OP1 DC C 6 NA NA C 102 1555 1555 2.82 LINK MG MG C 101 O HOH C 209 1555 1555 2.34 LINK MG MG C 101 O HOH C 223 1555 1555 1.91 LINK MG MG C 101 O HOH C 224 1555 1555 2.18 LINK MG MG C 101 O HOH D 213 1555 1555 2.17 LINK MG MG C 101 O HOH D 233 1555 1555 2.20 LINK NA NA C 102 O HOH C 230 1555 1555 2.23 LINK O HOH C 210 MG MG D 101 1565 1555 2.17 LINK O HOH C 221 NA NA D 103 1555 1555 2.49 LINK O HOH C 227 MG MG D 101 1565 1555 2.23 LINK O HOH C 233 MG MG D 101 1565 1555 2.04 LINK O2 BRU D 18 NA NA D 103 1555 1555 2.75 LINK O4' DI D 19 NA NA D 103 1555 1555 2.76 LINK MG MG D 101 O HOH D 228 1555 1555 2.07 LINK NA NA D 102 O HOH D 214 1555 1555 2.80 LINK NA NA D 103 O HOH D 237 1555 1555 2.47 SITE 1 AC1 6 HOH A 203 HOH A 231 HOH A 233 HOH B 106 SITE 2 AC1 6 HOH B 130 HOH B 134 SITE 1 AC2 6 DC A 6 DC A 7 DC B 16 DC B 17 SITE 2 AC2 6 HOH B 127 HOH B 128 SITE 1 AC3 6 HOH A 224 HOH C 209 HOH C 223 HOH C 224 SITE 2 AC3 6 HOH D 213 HOH D 233 SITE 1 AC4 5 DC B 11 HOH B 118 DI C 5 DC C 6 SITE 2 AC4 5 HOH C 230 SITE 1 AC5 4 HOH C 210 HOH C 227 HOH C 233 HOH D 228 SITE 1 AC6 3 HOH A 218 HOH B 123 HOH D 214 SITE 1 AC7 4 HOH C 221 BRU D 18 DI D 19 HOH D 237 SITE 1 AC8 15 DC A 2 DA A 3 DI A 4 DI A 5 SITE 2 AC8 15 NA A 102 HOH A 223 DC B 16 DI B 19 SITE 3 AC8 15 HOH B 109 HOH B 114 HOH B 115 HOH B 122 SITE 4 AC8 15 DI C 10 HOH C 211 HOH C 213 SITE 1 AC9 12 DC A 1 DC A 2 DA A 3 DI A 4 SITE 2 AC9 12 HOH A 223 DC B 17 DI B 20 HOH B 114 SITE 3 AC9 12 HOH B 116 HOH B 117 HOH B 121 HOH B 122 SITE 1 AD1 12 DI B 20 HOH B 103 HOH B 108 DC C 6 SITE 2 AD1 12 DI C 9 HOH C 206 HOH C 217 HOH C 218 SITE 3 AD1 12 DC D 12 DA D 13 DI D 14 DI D 15 SITE 1 AD2 12 DI B 20 DC C 7 DI C 10 HOH C 203 SITE 2 AD2 12 HOH C 206 HOH C 218 HOH C 219 HOH C 222 SITE 3 AD2 12 DC D 11 DC D 12 DA D 13 DI D 14 SITE 1 AD3 14 DI A 10 HOH A 202 HOH A 205 DC C 2 SITE 2 AD3 14 DA C 3 DI C 4 DI C 5 DC D 16 SITE 3 AD3 14 DI D 19 NA D 103 HOH D 215 HOH D 216 SITE 4 AD3 14 HOH D 223 HOH D 234 SITE 1 AD4 14 DI A 10 DC C 1 DC C 2 DA C 3 SITE 2 AD4 14 DI C 4 DC D 17 DI D 20 NA D 103 SITE 3 AD4 14 HOH D 205 HOH D 215 HOH D 223 HOH D 225 SITE 4 AD4 14 HOH D 226 HOH D 234 CRYST1 24.884 32.798 34.034 90.25 107.32 111.04 P 1 4 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 0.040186 0.015462 0.014577 0.00000 SCALE2 0.000000 0.032668 0.004112 0.00000 SCALE3 0.000000 0.000000 0.031021 0.00000