HEADER DNA 17-NOV-09 3KQ8 TITLE 5-TE-URIDINE DERIVATIZED DNA-8MER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*(UMS)P*GP*(TTI)P*AP*CP*AP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 5-TELLURIUM MODIFIED DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZE 5-TE-URIDINE AND INCORPORATED SOURCE 4 IT INTO DNA KEYWDS TELLURIUM DNA, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.SHENG,A.E.A.HASSAN,W.ZHANG,Z.HUANG REVDAT 1 17-NOV-10 3KQ8 0 JRNL AUTH J.SHENG,A.E.A.HASSAN,W.ZHANG,Z.HUANG JRNL TITL SYNTHESIS AND STRUCTURE STUDIES OF 5-TELLURIUM MODIFIED DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 2965 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.300 REMARK 3 FREE R VALUE TEST SET COUNT : 134 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 192 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 6 REMARK 3 BIN FREE R VALUE : 0.1700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 162 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.08000 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): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.900 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 181 ; 0.007 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 277 ; 1.531 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL 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): 32 ; 0.052 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 83 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 62 ; 0.139 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 107 ; 0.273 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 22 ; 0.177 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.993 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 22 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.100 ; 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): 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 262 ; 1.154 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 277 ; 1.438 ; 4.500 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 9 REMARK 3 ORIGIN FOR THE GROUP (A): 40.6005 30.1718 -0.9870 REMARK 3 T TENSOR REMARK 3 T11: -0.0025 T22: 0.0025 REMARK 3 T33: -0.0204 T12: 0.0032 REMARK 3 T13: -0.0101 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 10.0892 L22: 0.1978 REMARK 3 L33: 0.2103 L12: 1.4125 REMARK 3 L13: 1.4568 L23: 0.2040 REMARK 3 S TENSOR REMARK 3 S11: 0.0216 S12: 0.2862 S13: -0.0008 REMARK 3 S21: -0.0050 S22: -0.0122 S23: 0.0101 REMARK 3 S31: -0.0585 S32: -0.0434 S33: -0.0093 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 13 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3941 34.4537 -3.8004 REMARK 3 T TENSOR REMARK 3 T11: -0.0549 T22: -0.0268 REMARK 3 T33: -0.0473 T12: 0.0029 REMARK 3 T13: -0.0052 T23: 0.0172 REMARK 3 L TENSOR REMARK 3 L11: 5.4551 L22: 3.1225 REMARK 3 L33: 1.9382 L12: -1.9288 REMARK 3 L13: -0.5311 L23: 1.5510 REMARK 3 S TENSOR REMARK 3 S11: 0.0885 S12: 0.1148 S13: 0.0163 REMARK 3 S21: 0.1310 S22: -0.0537 S23: 0.0200 REMARK 3 S31: 0.1055 S32: -0.1385 S33: -0.0348 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 3KQ8 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-09. REMARK 100 THE RCSB ID CODE IS RCSB056310. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 99 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : SI(III) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3122 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 22.500 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.18600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 15.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V / V MPD, 40 MM NA CACODYLATE PH REMARK 280 7.0, 12 MM SPERMINE TETRA-HCL, 80 MM POTASSIUM CHLORIDE AND 20 MM REMARK 280 MAGNESIUM CHLORIDE, 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 11.96450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.12100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.12100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.94675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.12100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.12100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 5.98225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.12100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.12100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.94675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.12100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.12100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 5.98225 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 11.96450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 DG A 3 O5' - P - OP2 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG A 3 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DG A 3 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES 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 A 9 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 25 O REMARK 620 2 HOH A 37 O 108.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 TTI A 4 TE5 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 35 O REMARK 620 2 TTI A 4 C5 165.7 REMARK 620 N 1 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 9 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FA1 RELATED DB: PDB DBREF 3KQ8 A 1 8 PDB 3KQ8 3KQ8 1 8 SEQRES 1 A 8 DG UMS DG TTI DA DC DA DC MODRES 3KQ8 UMS A 2 DU MODRES 3KQ8 TTI A 4 DU HET UMS A 2 21 HET TTI A 4 20 HET MG A 9 1 HETNAM UMS 2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE HETNAM TTI 2'-DEOXY-5-TELLUROXOURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM MG MAGNESIUM ION HETSYN TTI 5-TELLURIUM-DEOXYURIDINE-5'-PHOSPHATE FORMUL 1 UMS C10 H15 N2 O8 P SE FORMUL 1 TTI C9 H13 N2 O8 P TE FORMUL 2 MG MG 2+ FORMUL 3 HOH *36(H2 O) LINK O3' DG A 1 P UMS A 2 1555 1555 1.60 LINK O3' UMS A 2 P DG A 3 1555 1555 1.61 LINK O3' DG A 3 P TTI A 4 1555 1555 1.60 LINK MG MG A 9 O HOH A 25 1555 1555 1.86 LINK MG MG A 9 O HOH A 37 1555 1555 1.89 LINK O3' TTI A 4 P DA A 5 1555 1555 1.59 LINK TE5 TTI A 4 O HOH A 35 1555 1555 2.37 SITE 1 AC1 4 UMS A 2 DG A 3 HOH A 25 HOH A 37 CRYST1 42.242 42.242 23.929 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 0.023673 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023673 0.000000 0.00000 SCALE3 0.000000 0.000000 0.041790 0.00000 ATOM 1 O5' DG A 1 44.387 34.764 5.379 1.00 11.06 O ATOM 2 C5' DG A 1 45.797 34.857 5.116 1.00 11.86 C ATOM 3 C4' DG A 1 46.331 33.658 4.347 1.00 11.68 C ATOM 4 O4' DG A 1 46.195 32.457 5.156 1.00 11.44 O ATOM 5 C3' DG A 1 45.609 33.303 3.052 1.00 11.52 C ATOM 6 O3' DG A 1 46.118 34.119 2.002 1.00 12.27 O ATOM 7 C2' DG A 1 45.997 31.830 2.902 1.00 11.47 C ATOM 8 C1' DG A 1 45.839 31.358 4.341 1.00 11.32 C ATOM 9 N9 DG A 1 44.468 30.948 4.657 1.00 11.68 N ATOM 10 C8 DG A 1 43.485 31.679 5.282 1.00 11.54 C ATOM 11 N7 DG A 1 42.355 31.036 5.406 1.00 12.25 N ATOM 12 C5 DG A 1 42.613 29.799 4.809 1.00 11.01 C ATOM 13 C6 DG A 1 41.777 28.671 4.631 1.00 11.02 C ATOM 14 O6 DG A 1 40.604 28.545 4.997 1.00 11.70 O ATOM 15 N1 DG A 1 42.437 27.610 3.988 1.00 11.02 N ATOM 16 C2 DG A 1 43.745 27.658 3.558 1.00 12.29 C ATOM 17 N2 DG A 1 44.233 26.563 2.959 1.00 12.54 N ATOM 18 N3 DG A 1 44.536 28.708 3.723 1.00 10.54 N ATOM 19 C4 DG A 1 43.903 29.735 4.335 1.00 10.82 C HETATM 20 P UMS A 2 45.187 34.585 0.789 1.00 11.64 P HETATM 21 OP1 UMS A 2 46.009 35.447 -0.069 1.00 11.77 O HETATM 22 OP2 UMS A 2 43.881 35.040 1.303 1.00 12.03 O HETATM 23 O5' UMS A 2 44.907 33.255 -0.049 1.00 11.28 O HETATM 24 C5' UMS A 2 45.922 32.613 -0.800 1.00 10.57 C HETATM 25 C4' UMS A 2 45.449 31.255 -1.265 1.00 12.64 C HETATM 26 O4' UMS A 2 45.079 30.429 -0.136 1.00 12.41 O HETATM 27 C3' UMS A 2 44.195 31.265 -2.127 1.00 14.22 C HETATM 28 O3' UMS A 2 44.542 31.649 -3.442 1.00 16.87 O HETATM 29 C2' UMS A 2 43.758 29.806 -2.014 1.00 14.05 C HETATM 30 SE2' UMS A 2 44.913 28.605 -3.081 1.00 15.73 SE HETATM 31 C1' UMS A 2 44.036 29.563 -0.532 1.00 13.07 C HETATM 32 CA' UMS A 2 43.932 26.909 -3.107 1.00 17.55 C HETATM 33 N1 UMS A 2 42.847 29.839 0.321 1.00 13.63 N HETATM 34 C2 UMS A 2 41.881 28.843 0.426 1.00 13.61 C HETATM 35 O2 UMS A 2 41.973 27.772 -0.155 1.00 13.74 O HETATM 36 N3 UMS A 2 40.814 29.154 1.243 1.00 12.01 N HETATM 37 C4 UMS A 2 40.625 30.347 1.928 1.00 12.26 C HETATM 38 O4 UMS A 2 39.618 30.490 2.604 1.00 11.98 O HETATM 39 C5 UMS A 2 41.666 31.344 1.775 1.00 12.65 C HETATM 40 C6 UMS A 2 42.718 31.058 0.986 1.00 12.76 C ATOM 41 P DG A 3 43.517 32.397 -4.431 1.00 17.88 P ATOM 42 OP1 DG A 3 44.288 32.623 -5.656 1.00 19.84 O ATOM 43 OP2 DG A 3 42.907 33.520 -3.693 1.00 19.81 O ATOM 44 O5' DG A 3 42.240 31.431 -4.584 1.00 20.13 O ATOM 45 C5' DG A 3 42.154 30.353 -5.486 1.00 20.14 C ATOM 46 C4' DG A 3 41.060 29.378 -5.060 1.00 16.04 C ATOM 47 O4' DG A 3 41.063 29.180 -3.623 1.00 15.24 O ATOM 48 C3' DG A 3 39.600 29.734 -5.321 1.00 14.35 C ATOM 49 O3' DG A 3 39.305 29.611 -6.694 1.00 13.11 O ATOM 50 C2' DG A 3 38.964 28.594 -4.531 1.00 13.65 C ATOM 51 C1' DG A 3 39.829 28.582 -3.266 1.00 12.41 C ATOM 52 N9 DG A 3 39.228 29.331 -2.166 1.00 12.12 N ATOM 53 C8 DG A 3 39.594 30.554 -1.663 1.00 11.58 C ATOM 54 N7 DG A 3 38.862 30.953 -0.663 1.00 11.79 N ATOM 55 C5 DG A 3 37.940 29.923 -0.492 1.00 11.50 C ATOM 56 C6 DG A 3 36.881 29.778 0.443 1.00 11.16 C ATOM 57 O6 DG A 3 36.547 30.567 1.339 1.00 11.58 O ATOM 58 N1 DG A 3 36.182 28.579 0.259 1.00 12.09 N ATOM 59 C2 DG A 3 36.476 27.629 -0.698 1.00 11.36 C ATOM 60 N2 DG A 3 35.704 26.537 -0.733 1.00 10.88 N ATOM 61 N3 DG A 3 37.472 27.754 -1.570 1.00 10.50 N ATOM 62 C4 DG A 3 38.154 28.919 -1.410 1.00 11.69 C HETATM 63 N1 TTI A 4 34.521 28.495 -3.603 1.00 11.65 N HETATM 64 C2 TTI A 4 33.623 28.588 -2.562 1.00 11.82 C HETATM 65 O2 TTI A 4 32.779 27.760 -2.332 1.00 11.40 O HETATM 66 N3 TTI A 4 33.717 29.711 -1.797 1.00 11.10 N HETATM 67 C4 TTI A 4 34.616 30.745 -1.961 1.00 12.15 C HETATM 68 O4 TTI A 4 34.625 31.724 -1.210 1.00 10.76 O HETATM 69 C5 TTI A 4 35.530 30.592 -3.073 1.00 10.78 C HETATM 70 C6 TTI A 4 35.459 29.488 -3.830 1.00 12.57 C HETATM 71 C1' TTI A 4 34.496 27.280 -4.480 1.00 12.38 C HETATM 72 C2' TTI A 4 33.422 27.295 -5.569 1.00 11.05 C HETATM 73 C3' TTI A 4 34.224 27.804 -6.763 1.00 11.78 C HETATM 74 O3' TTI A 4 33.689 27.381 -8.001 1.00 12.21 O HETATM 75 C4' TTI A 4 35.579 27.140 -6.548 1.00 12.65 C HETATM 76 O4' TTI A 4 35.760 27.188 -5.110 1.00 12.44 O HETATM 77 C5' TTI A 4 36.742 27.826 -7.244 1.00 12.89 C HETATM 78 O5' TTI A 4 36.811 29.199 -6.839 1.00 12.90 O HETATM 79 P TTI A 4 37.969 30.189 -7.349 1.00 12.84 P HETATM 80 O1P TTI A 4 37.711 31.513 -6.756 1.00 14.57 O HETATM 81 O2P TTI A 4 38.112 30.073 -8.809 1.00 13.15 O HETATM 82 TE5 TTI A 4 36.982 32.030 -3.455 0.75 15.87 TE ATOM 83 P DA A 5 32.535 28.217 -8.715 1.00 15.49 P ATOM 84 OP1 DA A 5 32.403 27.659 -10.080 1.00 16.09 O ATOM 85 OP2 DA A 5 32.739 29.665 -8.500 1.00 17.06 O ATOM 86 O5' DA A 5 31.257 27.801 -7.854 1.00 13.84 O ATOM 87 C5' DA A 5 30.184 28.669 -7.634 1.00 14.52 C ATOM 88 C4' DA A 5 29.365 28.123 -6.479 1.00 13.13 C ATOM 89 O4' DA A 5 30.201 28.026 -5.298 1.00 13.55 O ATOM 90 C3' DA A 5 28.214 29.025 -6.086 1.00 12.73 C ATOM 91 O3' DA A 5 27.083 28.630 -6.823 1.00 13.54 O ATOM 92 C2' DA A 5 28.036 28.724 -4.599 1.00 12.49 C ATOM 93 C1' DA A 5 29.490 28.540 -4.184 1.00 12.14 C ATOM 94 N9 DA A 5 30.171 29.753 -3.731 1.00 12.21 N ATOM 95 C8 DA A 5 31.219 30.384 -4.344 1.00 12.10 C ATOM 96 N7 DA A 5 31.659 31.430 -3.689 1.00 12.08 N ATOM 97 C5 DA A 5 30.849 31.487 -2.567 1.00 11.76 C ATOM 98 C6 DA A 5 30.807 32.367 -1.467 1.00 12.21 C ATOM 99 N6 DA A 5 31.630 33.394 -1.330 1.00 12.00 N ATOM 100 N1 DA A 5 29.868 32.150 -0.515 1.00 12.35 N ATOM 101 C2 DA A 5 29.041 31.105 -0.657 1.00 11.72 C ATOM 102 N3 DA A 5 28.997 30.207 -1.637 1.00 11.36 N ATOM 103 C4 DA A 5 29.928 30.455 -2.572 1.00 12.05 C ATOM 104 P DC A 6 26.064 29.729 -7.342 1.00 14.47 P ATOM 105 OP1 DC A 6 24.985 29.010 -8.065 1.00 14.24 O ATOM 106 OP2 DC A 6 26.837 30.819 -7.973 1.00 14.15 O ATOM 107 O5' DC A 6 25.421 30.286 -5.991 1.00 14.84 O ATOM 108 C5' DC A 6 24.487 29.513 -5.246 1.00 13.67 C ATOM 109 C4' DC A 6 24.194 30.216 -3.942 1.00 13.22 C ATOM 110 O4' DC A 6 25.406 30.331 -3.152 1.00 14.01 O ATOM 111 C3' DC A 6 23.757 31.663 -4.117 1.00 13.49 C ATOM 112 O3' DC A 6 22.399 31.713 -4.504 1.00 15.16 O ATOM 113 C2' DC A 6 23.973 32.177 -2.705 1.00 14.63 C ATOM 114 C1' DC A 6 25.331 31.543 -2.429 1.00 13.23 C ATOM 115 N1 DC A 6 26.493 32.416 -2.791 1.00 12.99 N ATOM 116 C2 DC A 6 26.856 33.430 -1.885 1.00 13.77 C ATOM 117 O2 DC A 6 26.205 33.560 -0.848 1.00 14.02 O ATOM 118 N3 DC A 6 27.920 34.223 -2.158 1.00 12.45 N ATOM 119 C4 DC A 6 28.614 34.052 -3.281 1.00 12.78 C ATOM 120 N4 DC A 6 29.650 34.870 -3.483 1.00 13.15 N ATOM 121 C5 DC A 6 28.256 33.036 -4.234 1.00 12.99 C ATOM 122 C6 DC A 6 27.200 32.250 -3.956 1.00 13.35 C ATOM 123 P DA A 7 21.810 33.009 -5.242 1.00 15.78 P ATOM 124 OP1 DA A 7 20.462 32.658 -5.764 1.00 17.09 O ATOM 125 OP2 DA A 7 22.830 33.543 -6.182 1.00 15.68 O ATOM 126 O5' DA A 7 21.638 34.033 -4.037 1.00 15.64 O ATOM 127 C5' DA A 7 20.770 33.802 -2.942 1.00 15.33 C ATOM 128 C4' DA A 7 20.872 35.015 -2.034 1.00 13.92 C ATOM 129 O4' DA A 7 22.199 35.100 -1.466 1.00 14.54 O ATOM 130 C3' DA A 7 20.720 36.354 -2.722 1.00 13.69 C ATOM 131 O3' DA A 7 19.344 36.650 -2.783 1.00 15.60 O ATOM 132 C2' DA A 7 21.464 37.331 -1.822 1.00 13.78 C ATOM 133 C1' DA A 7 22.603 36.457 -1.352 1.00 13.49 C ATOM 134 N9 DA A 7 23.868 36.593 -2.069 1.00 12.97 N ATOM 135 C8 DA A 7 24.318 35.844 -3.119 1.00 12.83 C ATOM 136 N7 DA A 7 25.518 36.181 -3.527 1.00 12.89 N ATOM 137 C5 DA A 7 25.896 37.210 -2.677 1.00 13.21 C ATOM 138 C6 DA A 7 27.076 37.996 -2.570 1.00 12.64 C ATOM 139 N6 DA A 7 28.144 37.851 -3.372 1.00 12.83 N ATOM 140 N1 DA A 7 27.111 38.950 -1.603 1.00 12.77 N ATOM 141 C2 DA A 7 26.046 39.092 -0.796 1.00 12.88 C ATOM 142 N3 DA A 7 24.900 38.410 -0.809 1.00 12.77 N ATOM 143 C4 DA A 7 24.885 37.474 -1.768 1.00 12.62 C ATOM 144 P DC A 8 18.792 37.625 -3.896 1.00 15.71 P ATOM 145 OP1 DC A 8 17.333 37.632 -3.690 1.00 16.27 O ATOM 146 OP2 DC A 8 19.320 37.184 -5.202 1.00 17.41 O ATOM 147 O5' DC A 8 19.376 39.070 -3.561 1.00 15.47 O ATOM 148 C5' DC A 8 18.866 39.745 -2.430 1.00 15.45 C ATOM 149 C4' DC A 8 19.597 41.039 -2.162 1.00 17.10 C ATOM 150 O4' DC A 8 21.008 40.747 -2.062 1.00 16.52 O ATOM 151 C3' DC A 8 19.412 42.103 -3.239 1.00 18.18 C ATOM 152 O3' DC A 8 19.171 43.348 -2.618 1.00 21.35 O ATOM 153 C2' DC A 8 20.737 42.123 -3.977 1.00 17.37 C ATOM 154 C1' DC A 8 21.714 41.626 -2.911 1.00 16.17 C ATOM 155 N1 DC A 8 22.888 40.956 -3.549 1.00 15.41 N ATOM 156 C2 DC A 8 24.172 41.490 -3.338 1.00 14.51 C ATOM 157 O2 DC A 8 24.307 42.478 -2.593 1.00 14.62 O ATOM 158 N3 DC A 8 25.229 40.900 -3.957 1.00 14.63 N ATOM 159 C4 DC A 8 25.046 39.829 -4.747 1.00 14.28 C ATOM 160 N4 DC A 8 26.113 39.289 -5.331 1.00 13.66 N ATOM 161 C5 DC A 8 23.751 39.271 -4.970 1.00 12.96 C ATOM 162 C6 DC A 8 22.717 39.866 -4.369 1.00 14.39 C TER 163 DC A 8 HETATM 164 MG MG A 9 32.508 37.550 -1.471 1.00 12.21 MG HETATM 165 O HOH A 10 42.712 25.200 -0.002 1.00 21.21 O HETATM 166 O HOH A 11 23.019 36.116 -7.159 1.00 26.34 O HETATM 167 O HOH A 12 41.579 34.640 0.024 1.00 22.46 O HETATM 168 O HOH A 13 20.077 29.516 -2.478 1.00 32.52 O HETATM 169 O HOH A 14 46.234 36.141 -2.515 1.00 22.36 O HETATM 170 O HOH A 15 47.554 39.377 -1.107 1.00 23.27 O HETATM 171 O HOH A 16 48.132 35.486 -4.031 1.00 28.15 O HETATM 172 O HOH A 17 26.988 35.558 -5.834 1.00 25.89 O HETATM 173 O HOH A 18 27.430 27.792 -1.337 1.00 10.11 O HETATM 174 O HOH A 19 35.564 36.986 -0.824 1.00 27.55 O HETATM 175 O HOH A 20 29.977 38.739 -6.023 1.00 25.80 O HETATM 176 O HOH A 21 43.186 36.328 3.613 1.00 26.28 O HETATM 177 O HOH A 22 31.087 34.605 -6.117 1.00 27.67 O HETATM 178 O HOH A 23 38.138 32.496 -10.433 1.00 46.38 O HETATM 179 O HOH A 24 18.438 34.701 -6.020 1.00 33.73 O HETATM 180 O HOH A 25 33.400 38.945 -0.632 1.00 19.47 O HETATM 181 O HOH A 26 34.287 40.287 -3.918 1.00 38.32 O HETATM 182 O HOH A 27 30.363 26.317 -11.171 1.00 26.77 O HETATM 183 O HOH A 28 35.092 32.798 -6.590 1.00 28.54 O HETATM 184 O HOH A 29 27.949 29.760 -10.459 1.00 28.51 O HETATM 185 O HOH A 30 27.616 33.627 -7.603 1.00 31.80 O HETATM 186 O HOH A 31 19.189 30.872 -4.536 1.00 32.00 O HETATM 187 O HOH A 32 29.962 32.367 -7.139 1.00 40.53 O HETATM 188 O HOH A 33 28.876 34.730 -9.779 1.00 38.44 O HETATM 189 O HOH A 34 28.463 37.389 -9.738 1.00 36.52 O HETATM 190 O HOH A 35 38.591 33.770 -3.309 1.00 27.20 O HETATM 191 O HOH A 36 41.368 33.232 -2.090 1.00 22.06 O HETATM 192 O HOH A 37 32.524 37.864 -3.333 1.00 2.00 O HETATM 193 O HOH A 38 22.595 39.758 0.293 1.00 16.47 O HETATM 194 O HOH A 39 37.828 25.635 -3.414 1.00 16.80 O HETATM 195 O HOH A 40 46.848 37.925 0.926 1.00 15.11 O HETATM 196 O HOH A 41 16.695 42.285 -1.113 1.00 20.66 O HETATM 197 O HOH A 42 25.228 26.695 -2.550 1.00 15.02 O HETATM 198 O HOH A 43 25.474 37.272 -7.269 1.00 16.01 O HETATM 199 O HOH A 44 22.656 27.851 -1.979 1.00 16.08 O HETATM 200 O HOH A 45 33.390 33.402 -4.569 1.00 22.25 O CONECT 6 20 CONECT 20 6 21 22 23 CONECT 21 20 CONECT 22 20 CONECT 23 20 24 CONECT 24 23 25 CONECT 25 24 26 27 CONECT 26 25 31 CONECT 27 25 28 29 CONECT 28 27 41 CONECT 29 27 30 31 CONECT 30 29 32 CONECT 31 26 29 33 CONECT 32 30 CONECT 33 31 34 40 CONECT 34 33 35 36 CONECT 35 34 CONECT 36 34 37 CONECT 37 36 38 39 CONECT 38 37 CONECT 39 37 40 CONECT 40 33 39 CONECT 41 28 CONECT 49 79 CONECT 63 64 70 71 CONECT 64 63 65 66 CONECT 65 64 CONECT 66 64 67 CONECT 67 66 68 69 CONECT 68 67 CONECT 69 67 70 82 CONECT 70 63 69 CONECT 71 63 72 76 CONECT 72 71 73 CONECT 73 72 74 75 CONECT 74 73 83 CONECT 75 73 76 77 CONECT 76 71 75 CONECT 77 75 78 CONECT 78 77 79 CONECT 79 49 78 80 81 CONECT 80 79 CONECT 81 79 CONECT 82 69 190 CONECT 83 74 CONECT 164 180 192 CONECT 180 164 CONECT 190 82 CONECT 192 164 MASTER 338 0 3 0 0 0 1 6 199 1 49 1 END