HEADER DNA 04-AUG-09 3IJN TITLE 5-SEME-CYTIDINE MODIFIED DNA 8MER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*(UMS)P*GP*TP*AP*(5SE)P*AP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 5-SEME-CYTIDINE-DNA OCTAMER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS SELENIUM, DNA, 5-SEME-CYTIDINE EXPDTA X-RAY DIFFRACTION AUTHOR J.SHENG,W.ZHANG,A.E.A.HASSAN,J.GAN,Z.HUANG REVDAT 3 06-SEP-23 3IJN 1 LINK REVDAT 2 13-JUL-11 3IJN 1 VERSN REVDAT 1 06-OCT-09 3IJN 0 JRNL AUTH J.SHENG,W.ZHANG,A.E.A.HASSAN,J.GAN,Z.HUANG JRNL TITL 5-SEME-CYTIDINE MODIFIED DNA 8MER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 2159 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 104 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) : 134 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3520 REMARK 3 BIN FREE R VALUE SET COUNT : 9 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 164 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.76000 REMARK 3 B22 (A**2) : 0.76000 REMARK 3 B33 (A**2) : -1.51000 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): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.334 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 181 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 272 ; 2.042 ; 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): 29 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 92 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 61 ; 0.342 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 97 ; 0.279 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 23 ; 0.150 ; 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): 20 ; 0.192 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.135 ; 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 264 ; 0.646 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 272 ; 0.814 ; 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 : 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 4 REMARK 3 ORIGIN FOR THE GROUP (A): 12.2728 40.9982 5.2746 REMARK 3 T TENSOR REMARK 3 T11: 0.2447 T22: 0.2449 REMARK 3 T33: 0.2224 T12: -0.0276 REMARK 3 T13: -0.0236 T23: -0.0459 REMARK 3 L TENSOR REMARK 3 L11: 0.1734 L22: 6.1739 REMARK 3 L33: 1.0527 L12: -0.9801 REMARK 3 L13: -0.3874 L23: 1.8459 REMARK 3 S TENSOR REMARK 3 S11: 0.1210 S12: 0.3224 S13: 0.1581 REMARK 3 S21: -0.2993 S22: -0.0007 S23: -0.1882 REMARK 3 S31: -0.1642 S32: -0.1250 S33: -0.1203 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 8 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8407 25.7755 2.2939 REMARK 3 T TENSOR REMARK 3 T11: 0.1567 T22: 0.1581 REMARK 3 T33: 0.1450 T12: 0.0112 REMARK 3 T13: -0.0466 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 5.1849 L22: 10.3167 REMARK 3 L33: 7.4352 L12: 0.4017 REMARK 3 L13: -1.6536 L23: -0.5501 REMARK 3 S TENSOR REMARK 3 S11: -0.1334 S12: -0.1405 S13: -0.1907 REMARK 3 S21: -0.4170 S22: -0.0214 S23: -0.1579 REMARK 3 S31: 0.4675 S32: 0.2088 S33: 0.1548 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 3IJN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054494. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-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 : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : HORIZONTALLY FOCUSING REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2282 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 15.60 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.1600 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 (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.44500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.890 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: 1DNS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V / V MPD, 40 MM NA CACODYLATE PH REMARK 280 7.0, 12 MM SPERMINE TETRA-HCL, 40 MM LITHIUM CHLORIDE, 80 MM REMARK 280 STRONTIUM CHLORIDE / 20 MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 12.27400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.29050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.29050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.41100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.29050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.29050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 6.13700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.29050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.29050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 18.41100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.29050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.29050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 6.13700 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 12.27400 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 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 42.58100 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 42.58100 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 12.27400 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DA A 5 O3' DA A 5 C3' -0.045 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 DG A 3 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 DA A 5 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 5SE A 6 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DA A 7 O3' - P - OP1 ANGL. DEV. = 9.2 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IJK RELATED DB: PDB DBREF 3IJN A 1 8 PDB 3IJN 3IJN 1 8 SEQRES 1 A 8 DG UMS DG DT DA 5SE DA DC MODRES 3IJN UMS A 2 DU MODRES 3IJN 5SE A 6 DU HET UMS A 2 21 HET 5SE A 6 21 HETNAM UMS 2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE HETNAM 5SE 2'-DEOXY-5-(METHYLSELANYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 5SE PHOSPHATE) FORMUL 1 UMS C10 H15 N2 O8 P SE FORMUL 1 5SE C10 H16 N3 O7 P SE FORMUL 2 HOH *34(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 1.60 LINK O3' DA A 5 P 5SE A 6 1555 1555 1.64 LINK O3' 5SE A 6 P DA A 7 1555 1555 1.60 CRYST1 42.581 42.581 24.548 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 0.023485 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.040737 0.00000 ATOM 1 O5' DG A 1 7.754 44.801 11.725 1.00 6.43 O ATOM 2 C5' DG A 1 7.629 46.197 11.469 1.00 6.35 C ATOM 3 C4' DG A 1 8.793 46.738 10.649 1.00 6.85 C ATOM 4 O4' DG A 1 10.019 46.600 11.412 1.00 7.12 O ATOM 5 C3' DG A 1 9.100 46.043 9.327 1.00 6.84 C ATOM 6 O3' DG A 1 8.292 46.546 8.268 1.00 6.71 O ATOM 7 C2' DG A 1 10.570 46.408 9.141 1.00 6.63 C ATOM 8 C1' DG A 1 11.097 46.270 10.563 1.00 6.53 C ATOM 9 N9 DG A 1 11.548 44.921 10.895 1.00 6.85 N ATOM 10 C8 DG A 1 10.833 43.954 11.566 1.00 6.83 C ATOM 11 N7 DG A 1 11.480 42.834 11.716 1.00 6.81 N ATOM 12 C5 DG A 1 12.702 43.071 11.104 1.00 6.37 C ATOM 13 C6 DG A 1 13.818 42.217 10.961 1.00 6.24 C ATOM 14 O6 DG A 1 13.936 41.055 11.360 1.00 6.70 O ATOM 15 N1 DG A 1 14.872 42.831 10.285 1.00 6.70 N ATOM 16 C2 DG A 1 14.835 44.118 9.806 1.00 6.58 C ATOM 17 N2 DG A 1 15.941 44.527 9.180 1.00 6.85 N ATOM 18 N3 DG A 1 13.793 44.939 9.929 1.00 6.46 N ATOM 19 C4 DG A 1 12.762 44.350 10.588 1.00 6.34 C HETATM 20 P UMS A 2 7.867 45.620 7.031 1.00 6.73 P HETATM 21 OP1 UMS A 2 6.960 46.398 6.159 1.00 5.92 O HETATM 22 OP2 UMS A 2 7.405 44.328 7.571 1.00 6.41 O HETATM 23 O5' UMS A 2 9.262 45.365 6.286 1.00 6.34 O HETATM 24 C5' UMS A 2 9.874 46.361 5.467 1.00 6.12 C HETATM 25 C4' UMS A 2 11.238 45.910 4.982 1.00 6.72 C HETATM 26 O4' UMS A 2 12.063 45.587 6.125 1.00 7.31 O HETATM 27 C3' UMS A 2 11.278 44.624 4.165 1.00 7.70 C HETATM 28 O3' UMS A 2 10.872 44.836 2.805 1.00 8.73 O HETATM 29 C2' UMS A 2 12.746 44.208 4.319 1.00 7.29 C HETATM 30 SE2' UMS A 2 13.960 45.301 3.207 0.70 9.24 SE HETATM 31 C1' UMS A 2 12.944 44.519 5.805 1.00 7.21 C HETATM 32 CA' UMS A 2 15.786 44.645 3.482 0.70 7.01 C HETATM 33 N1 UMS A 2 12.677 43.311 6.667 1.00 6.87 N HETATM 34 C2 UMS A 2 13.643 42.323 6.751 1.00 6.20 C HETATM 35 O2 UMS A 2 14.710 42.374 6.177 1.00 6.87 O HETATM 36 N3 UMS A 2 13.321 41.253 7.545 1.00 5.45 N HETATM 37 C4 UMS A 2 12.149 41.068 8.253 1.00 6.31 C HETATM 38 O4 UMS A 2 12.006 40.050 8.921 1.00 6.76 O HETATM 39 C5 UMS A 2 11.179 42.131 8.125 1.00 6.46 C HETATM 40 C6 UMS A 2 11.475 43.185 7.353 1.00 6.75 C ATOM 41 P DG A 3 10.001 43.752 2.012 1.00 8.67 P ATOM 42 OP1 DG A 3 9.613 44.425 0.762 1.00 8.68 O ATOM 43 OP2 DG A 3 8.986 43.181 2.928 1.00 9.19 O ATOM 44 O5' DG A 3 10.984 42.529 1.720 1.00 7.93 O ATOM 45 C5' DG A 3 12.122 42.676 0.899 1.00 7.39 C ATOM 46 C4' DG A 3 13.150 41.596 1.210 1.00 6.87 C ATOM 47 O4' DG A 3 13.468 41.594 2.623 1.00 5.78 O ATOM 48 C3' DG A 3 12.774 40.144 0.931 1.00 6.18 C ATOM 49 O3' DG A 3 12.833 39.851 -0.469 1.00 6.07 O ATOM 50 C2' DG A 3 13.928 39.489 1.677 1.00 5.69 C ATOM 51 C1' DG A 3 14.034 40.345 2.927 1.00 5.46 C ATOM 52 N9 DG A 3 13.282 39.748 4.019 1.00 5.62 N ATOM 53 C8 DG A 3 12.056 40.123 4.521 1.00 5.34 C ATOM 54 N7 DG A 3 11.648 39.366 5.503 1.00 5.20 N ATOM 55 C5 DG A 3 12.676 38.432 5.659 1.00 5.84 C ATOM 56 C6 DG A 3 12.825 37.347 6.564 1.00 5.22 C ATOM 57 O6 DG A 3 12.042 36.992 7.454 1.00 5.95 O ATOM 58 N1 DG A 3 14.014 36.642 6.366 1.00 4.87 N ATOM 59 C2 DG A 3 14.961 36.944 5.416 1.00 4.82 C ATOM 60 N2 DG A 3 16.055 36.174 5.369 1.00 5.28 N ATOM 61 N3 DG A 3 14.844 37.955 4.568 1.00 5.42 N ATOM 62 C4 DG A 3 13.684 38.650 4.742 1.00 5.83 C ATOM 63 P DT A 4 12.246 38.512 -1.133 1.00 6.47 P ATOM 64 OP1 DT A 4 12.338 38.640 -2.604 1.00 6.14 O ATOM 65 OP2 DT A 4 10.927 38.265 -0.524 1.00 6.69 O ATOM 66 O5' DT A 4 13.218 37.351 -0.611 1.00 7.07 O ATOM 67 C5' DT A 4 14.610 37.275 -0.918 1.00 6.72 C ATOM 68 C4' DT A 4 15.232 36.026 -0.305 1.00 6.64 C ATOM 69 O4' DT A 4 15.275 36.157 1.137 1.00 6.50 O ATOM 70 C3' DT A 4 14.481 34.716 -0.517 1.00 6.62 C ATOM 71 O3' DT A 4 14.766 34.153 -1.782 1.00 7.50 O ATOM 72 C2' DT A 4 15.037 33.857 0.611 1.00 5.84 C ATOM 73 C1' DT A 4 15.116 34.875 1.735 1.00 5.73 C ATOM 74 N1 DT A 4 13.907 34.877 2.623 1.00 6.26 N ATOM 75 C2 DT A 4 13.800 33.951 3.645 1.00 5.33 C ATOM 76 O2 DT A 4 14.634 33.102 3.882 1.00 5.72 O ATOM 77 N3 DT A 4 12.662 34.053 4.399 1.00 4.70 N ATOM 78 C4 DT A 4 11.635 34.960 4.232 1.00 5.19 C ATOM 79 O4 DT A 4 10.667 34.944 4.976 1.00 5.54 O ATOM 80 C5 DT A 4 11.790 35.900 3.138 1.00 5.70 C ATOM 81 C7 DT A 4 10.766 36.951 2.830 1.00 4.91 C ATOM 82 C6 DT A 4 12.905 35.812 2.404 1.00 6.43 C ATOM 83 P DA A 5 13.858 32.995 -2.418 1.00 7.49 P ATOM 84 OP1 DA A 5 14.216 32.947 -3.853 1.00 8.70 O ATOM 85 OP2 DA A 5 12.448 33.121 -1.966 1.00 7.75 O ATOM 86 O5' DA A 5 14.443 31.673 -1.751 1.00 7.10 O ATOM 87 C5' DA A 5 13.594 30.611 -1.433 1.00 5.26 C ATOM 88 C4' DA A 5 14.209 29.834 -0.297 1.00 4.89 C ATOM 89 O4' DA A 5 14.291 30.652 0.890 1.00 5.08 O ATOM 90 C3' DA A 5 13.374 28.649 0.102 1.00 5.11 C ATOM 91 O3' DA A 5 13.635 27.535 -0.659 1.00 24.95 O ATOM 92 C2' DA A 5 13.631 28.489 1.587 1.00 4.50 C ATOM 93 C1' DA A 5 13.782 29.939 2.001 1.00 4.18 C ATOM 94 N9 DA A 5 12.563 30.609 2.442 1.00 4.28 N ATOM 95 C8 DA A 5 11.964 31.674 1.833 1.00 3.70 C ATOM 96 N7 DA A 5 10.897 32.102 2.454 1.00 4.35 N ATOM 97 C5 DA A 5 10.790 31.272 3.557 1.00 4.41 C ATOM 98 C6 DA A 5 9.859 31.208 4.617 1.00 4.12 C ATOM 99 N6 DA A 5 8.821 32.037 4.738 1.00 3.75 N ATOM 100 N1 DA A 5 10.041 30.252 5.557 1.00 3.87 N ATOM 101 C2 DA A 5 11.079 29.410 5.440 1.00 3.60 C ATOM 102 N3 DA A 5 12.021 29.379 4.492 1.00 4.45 N ATOM 103 C4 DA A 5 11.816 30.342 3.571 1.00 4.47 C HETATM 104 P 5SE A 6 12.611 26.315 -1.037 1.00 26.63 P HETATM 105 N1 5SE A 6 9.764 26.760 3.384 1.00 24.16 N HETATM 106 C2 5SE A 6 8.708 27.066 4.229 1.00 25.26 C HETATM 107 O2 5SE A 6 8.535 26.355 5.208 1.00 27.44 O HETATM 108 N3 5SE A 6 7.880 28.103 3.983 1.00 23.81 N HETATM 109 C4 5SE A 6 8.097 28.828 2.921 1.00 21.58 C HETATM 110 N4 5SE A 6 7.259 29.832 2.723 1.00 21.26 N HETATM 111 C5 5SE A 6 9.188 28.535 2.056 1.00 23.72 C HETATM 112 C6 5SE A 6 10.000 27.508 2.299 1.00 23.78 C HETATM 113 C1' 5SE A 6 10.641 25.694 3.754 1.00 25.00 C HETATM 114 C2' 5SE A 6 10.150 24.292 3.532 1.00 25.84 C HETATM 115 OP2 5SE A 6 11.496 26.977 -1.691 1.00 26.59 O HETATM 116 C3' 5SE A 6 10.738 24.156 2.156 1.00 27.34 C HETATM 117 O3' 5SE A 6 10.683 22.800 1.748 1.00 31.01 O HETATM 118 C4' 5SE A 6 12.150 24.651 2.366 1.00 26.74 C HETATM 119 O4' 5SE A 6 11.807 25.902 2.987 1.00 28.09 O HETATM 120 C5' 5SE A 6 12.962 24.929 1.113 1.00 24.59 C HETATM 121 O5' 5SE A 6 12.157 25.777 0.370 1.00 24.94 O HETATM 122 CA5 5SE A 6 8.095 29.110 -0.855 1.00 29.51 C HETATM 123 SE5 5SE A 6 9.463 29.597 0.481 1.00 33.73 SE HETATM 124 OP1 5SE A 6 13.343 25.208 -1.665 1.00 31.76 O ATOM 125 P DA A 7 9.515 22.092 0.920 1.00 28.23 P ATOM 126 OP1 DA A 7 9.736 20.685 0.341 1.00 9.83 O ATOM 127 OP2 DA A 7 9.130 23.155 0.043 1.00 11.44 O ATOM 128 O5' DA A 7 8.395 21.974 2.070 1.00 9.28 O ATOM 129 C5' DA A 7 8.462 20.994 3.087 1.00 8.81 C ATOM 130 C4' DA A 7 7.275 21.131 4.015 1.00 7.62 C ATOM 131 O4' DA A 7 7.230 22.478 4.527 1.00 7.75 O ATOM 132 C3' DA A 7 5.923 20.962 3.363 1.00 7.48 C ATOM 133 O3' DA A 7 5.606 19.613 3.348 1.00 7.13 O ATOM 134 C2' DA A 7 5.001 21.711 4.313 1.00 7.52 C ATOM 135 C1' DA A 7 5.888 22.879 4.712 1.00 7.50 C ATOM 136 N9 DA A 7 5.699 24.127 3.974 1.00 7.67 N ATOM 137 C8 DA A 7 6.434 24.575 2.908 1.00 7.12 C ATOM 138 N7 DA A 7 6.057 25.744 2.463 1.00 6.73 N ATOM 139 C5 DA A 7 5.003 26.096 3.297 1.00 7.57 C ATOM 140 C6 DA A 7 4.157 27.233 3.370 1.00 7.76 C ATOM 141 N6 DA A 7 4.247 28.273 2.540 1.00 7.67 N ATOM 142 N1 DA A 7 3.195 27.267 4.330 1.00 7.67 N ATOM 143 C2 DA A 7 3.086 26.228 5.169 1.00 7.14 C ATOM 144 N3 DA A 7 3.826 25.115 5.198 1.00 7.86 N ATOM 145 C4 DA A 7 4.772 25.109 4.238 1.00 7.26 C ATOM 146 P DC A 8 4.684 19.045 2.193 1.00 7.24 P ATOM 147 OP1 DC A 8 4.687 17.574 2.325 1.00 7.43 O ATOM 148 OP2 DC A 8 5.074 19.720 0.939 1.00 7.48 O ATOM 149 O5' DC A 8 3.220 19.548 2.568 1.00 9.05 O ATOM 150 C5' DC A 8 2.554 19.020 3.710 1.00 9.67 C ATOM 151 C4' DC A 8 1.285 19.802 3.950 1.00 10.31 C ATOM 152 O4' DC A 8 1.653 21.189 4.102 1.00 11.03 O ATOM 153 C3' DC A 8 0.330 19.725 2.769 1.00 11.05 C ATOM 154 O3' DC A 8 -0.729 18.827 3.081 1.00 11.89 O ATOM 155 C2' DC A 8 -0.188 21.148 2.578 1.00 11.03 C ATOM 156 C1' DC A 8 0.715 22.014 3.447 1.00 10.15 C ATOM 157 N1 DC A 8 1.384 23.092 2.648 1.00 9.85 N ATOM 158 C2 DC A 8 0.848 24.381 2.726 1.00 10.19 C ATOM 159 O2 DC A 8 -0.134 24.581 3.456 1.00 10.07 O ATOM 160 N3 DC A 8 1.421 25.378 2.000 1.00 9.76 N ATOM 161 C4 DC A 8 2.476 25.125 1.224 1.00 9.42 C ATOM 162 N4 DC A 8 2.987 26.151 0.542 1.00 8.90 N ATOM 163 C5 DC A 8 3.043 23.816 1.128 1.00 9.13 C ATOM 164 C6 DC A 8 2.466 22.841 1.846 1.00 9.64 C TER 165 DC A 8 HETATM 166 O HOH A 9 -0.375 25.029 6.562 1.00 34.60 O HETATM 167 O HOH A 10 8.065 41.895 5.860 1.00 31.23 O HETATM 168 O HOH A 11 14.498 27.766 4.831 1.00 19.24 O HETATM 169 O HOH A 12 5.837 25.999 -0.473 1.00 31.96 O HETATM 170 O HOH A 13 15.590 25.473 3.813 1.00 27.19 O HETATM 171 O HOH A 14 15.771 24.483 -1.175 1.00 30.87 O HETATM 172 O HOH A 15 8.991 39.280 6.430 1.00 32.36 O HETATM 173 O HOH A 16 14.370 23.074 4.220 1.00 35.68 O HETATM 174 O HOH A 17 10.303 35.207 -0.382 1.00 39.03 O HETATM 175 O HOH A 18 9.188 33.817 1.308 1.00 24.26 O HETATM 176 O HOH A 19 9.967 37.822 9.033 1.00 22.56 O HETATM 177 O HOH A 20 8.059 36.172 5.256 1.00 32.79 O HETATM 178 O HOH A 21 10.104 40.758 12.838 1.00 31.45 O HETATM 179 O HOH A 22 6.003 32.217 0.732 1.00 34.97 O HETATM 180 O HOH A 23 8.833 25.387 -1.406 1.00 34.26 O HETATM 181 O HOH A 24 13.220 25.109 -4.615 1.00 42.84 O HETATM 182 O HOH A 25 9.448 47.819 1.049 1.00 41.29 O HETATM 183 O HOH A 26 6.462 43.438 9.872 1.00 31.32 O HETATM 184 O HOH A 27 16.896 38.517 2.915 1.00 33.26 O HETATM 185 O HOH A 28 7.563 18.401 -0.554 1.00 45.06 O HETATM 186 O HOH A 29 8.920 39.682 0.396 1.00 44.71 O HETATM 187 O HOH A 30 2.563 22.909 6.556 1.00 25.61 O HETATM 188 O HOH A 31 11.636 32.458 -5.583 1.00 39.36 O HETATM 189 O HOH A 32 5.485 22.405 -1.115 1.00 41.80 O HETATM 190 O HOH A 33 10.217 31.637 -2.269 1.00 34.47 O HETATM 191 O HOH A 34 6.338 16.037 3.754 1.00 34.72 O HETATM 192 O HOH A 35 16.543 25.957 1.206 1.00 23.06 O HETATM 193 O HOH A 36 15.978 43.594 -0.437 1.00 44.69 O HETATM 194 O HOH A 37 7.001 40.895 9.934 1.00 41.13 O HETATM 195 O HOH A 38 4.676 44.108 4.695 1.00 45.76 O HETATM 196 O HOH A 39 6.132 44.735 2.942 1.00 42.99 O HETATM 197 O HOH A 40 10.491 43.591 -2.466 1.00 46.85 O HETATM 198 O HOH A 41 12.442 39.172 12.582 1.00 34.40 O HETATM 199 O HOH A 42 10.653 29.456 -3.071 1.00 30.21 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 91 104 CONECT 104 91 115 121 124 CONECT 105 106 112 113 CONECT 106 105 107 108 CONECT 107 106 CONECT 108 106 109 CONECT 109 108 110 111 CONECT 110 109 CONECT 111 109 112 123 CONECT 112 105 111 CONECT 113 105 114 119 CONECT 114 113 116 CONECT 115 104 CONECT 116 114 117 118 CONECT 117 116 125 CONECT 118 116 119 120 CONECT 119 113 118 CONECT 120 118 121 CONECT 121 104 120 CONECT 122 123 CONECT 123 111 122 CONECT 124 104 CONECT 125 117 MASTER 340 0 2 0 0 0 0 6 198 1 46 1 END