PDB Short entry for 3UYB HEADER DNA 06-DEC-11 3UYB TITLE X-RAY CRYSTAL STRUCTURE OF THE RUTHENIUM COMPLEX [RU(TAP)2(DPPZ)]2+ TITLE 2 BOUND TO D(TCGGTACCGA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA-RUTHENIUM COMPLEX, SEMIINTERCALATION, INTERCALATION, MINOR GROOVE KEYWDS 2 INTERACTION, DNA EXPDTA X-RAY DIFFRACTION AUTHOR H.N.NIYAZI,S.C.M.TEXEIRA,E.P.MITCHELL,J.C.CARDIN,V.T.FORSYTH REVDAT 4 20-MAR-24 3UYB 1 REMARK LINK REVDAT 3 08-NOV-17 3UYB 1 REMARK REVDAT 2 29-APR-15 3UYB 1 SPRSDE REVDAT 1 16-JAN-13 3UYB 0 SPRSDE 29-APR-15 3UYB 3UYA JRNL AUTH H.N.NIYAZI,K.O'SULLIVAN,S.C.M.TEXEIRA,E.P.MITCHELL, JRNL AUTH 2 J.M.KELLY,J.C.CARDIN,V.T.FORSYTH JRNL TITL CRYSTAL STRUCTURE OF LAMBDA-[RU(TAP)2(DPPZ)]2+ WITH JRNL TITL 2 D(TCGGTACCGA)2 DISPLAYING KINKING OF DNA VIA JRNL TITL 3 SEMIINTERCALATION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.700 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 6591 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 316 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 365 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.1360 REMARK 3 BIN FREE R VALUE SET COUNT : 13 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 202 REMARK 3 HETEROGEN ATOMS : 103 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.11000 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): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.034 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.074 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 360 ; 0.034 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 576 ; 3.537 ; 1.993 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): 31 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 211 ; 0.038 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 360 ; 9.612 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 16 ;25.876 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 360 ;13.777 ; 5.000 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 10 REMARK 3 RESIDUE RANGE : A 11 A 13 REMARK 3 RESIDUE RANGE : A 14 A 87 REMARK 3 ORIGIN FOR THE GROUP (A): -42.417 -39.996 16.947 REMARK 3 T TENSOR REMARK 3 T11: 0.0093 T22: 0.0075 REMARK 3 T33: 0.0013 T12: 0.0022 REMARK 3 T13: 0.0022 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.0001 L22: 0.0002 REMARK 3 L33: 0.0002 L12: -0.0001 REMARK 3 L13: 0.0001 L23: 0.0001 REMARK 3 S TENSOR REMARK 3 S11: -0.0010 S12: -0.0004 S13: -0.0003 REMARK 3 S21: 0.0004 S22: 0.0010 S23: 0.0004 REMARK 3 S31: -0.0009 S32: 0.0007 S33: -0.0001 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3UYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069361. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98400 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7382 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 38.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10%(V/V) 2-METHYL-2,4-PENTANEDIOL, REMARK 280 40MM SODIUM CACODYLATE, 12MM SPERMINE TETRA-HCL, 80MM SODIUM REMARK 280 CHLORIDE, 20MM BARIUM CHLORIDE, 1MM DNA D(TCGGTACCGA), 1MM REMARK 280 LAMBDA-[RU(TAP)2DPPZ)CL2 , PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 14.49750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.18800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.18800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.74625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.18800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.18800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 7.24875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.18800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.18800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.74625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.18800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.18800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 7.24875 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 14.49750 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: 950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 28.99500 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 DT A 1 O3' DC A 2 P 0.124 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 DT A 1 C3' - O3' - P ANGL. DEV. = -16.0 DEGREES REMARK 500 DC A 2 O5' - P - OP1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC A 7 O4' - C4' - C3' ANGL. DEV. = -3.2 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 BA A 13 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 4 O6 REMARK 620 2 DT A 5 O4 67.9 REMARK 620 3 HOH A 20 O 66.3 114.6 REMARK 620 4 HOH A 28 O 96.9 76.0 66.3 REMARK 620 5 HOH A 35 O 142.8 75.7 126.4 66.2 REMARK 620 6 HOH A 45 O 127.5 105.3 139.5 133.3 69.0 REMARK 620 7 HOH A 49 O 135.0 154.9 75.9 89.0 79.8 70.5 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 RKL A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RKL A 12 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA A 13 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QRN RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF THE RUTHENIUM COMPLEX [RU(TAP)2(DPPZ)]2+ REMARK 900 BOUND TO D(TCGGCGCCGA)AT HIGH RESOLUTION. REMARK 900 RELATED ID: 3QF8 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF THE RUTHENIUM COMPLEX [RU(TAP)2(DPPZ)]2+ REMARK 900 BOUND TO D(TCGGCGCCGA) AT MEDIUM RESOLUTION. REMARK 900 RELATED ID: 3GOM RELATED DB: PDB REMARK 900 BARIUM BOUND TO THE HOLLIDAY JUNCTION SEQUENCE D(TCGGCGCCGA)4. REMARK 900 RELATED ID: 3UYA RELATED DB: PDB DBREF 3UYB A 1 10 PDB 3UYB 3UYB 1 10 SEQRES 1 A 10 DT DC DG DG DT DA DC DC DG DA HET RKL A 11 51 HET RKL A 12 51 HET BA A 13 1 HETNAM RKL RU(TAP)2(DPPZ) COMPLEX HETNAM BA BARIUM ION FORMUL 2 RKL 2(C38 H22 N12 RU 2+) FORMUL 4 BA BA 2+ FORMUL 5 HOH *66(H2 O) LINK O6 DG A 4 BA BA A 13 1555 1555 2.84 LINK O4 DT A 5 BA BA A 13 1555 1555 2.85 LINK BA BA A 13 O HOH A 20 1555 1555 2.76 LINK BA BA A 13 O HOH A 28 1555 1555 2.83 LINK BA BA A 13 O HOH A 35 1555 1555 2.89 LINK BA BA A 13 O HOH A 45 1555 1555 2.86 LINK BA BA A 13 O HOH A 49 1555 1555 2.87 SITE 1 AC1 11 DT A 1 DC A 2 DG A 4 DT A 5 SITE 2 AC1 11 DA A 6 DC A 7 HOH A 14 HOH A 15 SITE 3 AC1 11 HOH A 58 HOH A 82 HOH A 84 SITE 1 AC2 12 DT A 1 DC A 2 DG A 3 DG A 4 SITE 2 AC2 12 DC A 7 DC A 8 DG A 9 DA A 10 SITE 3 AC2 12 HOH A 16 HOH A 19 HOH A 41 HOH A 51 SITE 1 AC3 8 DG A 3 DG A 4 DT A 5 HOH A 20 SITE 2 AC3 8 HOH A 28 HOH A 35 HOH A 45 HOH A 49 CRYST1 54.376 54.376 28.995 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 0.018390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018390 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034489 0.00000