PDB Full entry for 4H5A HEADER DNA 18-SEP-12 4H5A TITLE DNA OCTAMER D (GTSEGTACAC) PARTIALLY CROSSLINKED WITH PLATINUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*(2ST)P*GP*GP*CP*CP*AP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: SHORT DNA 8MER WITH SE MODIFICATION SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS SELENIUM MODIFICATION TO FACILITATE CRYSTALLIZATION, DNA EXPDTA X-RAY DIFFRACTION AUTHOR W.ZHANG,G.CORONADO,Z.HUANG REVDAT 2 28-FEB-24 4H5A 1 REMARK LINK REVDAT 1 03-OCT-12 4H5A 0 JRNL AUTH W.ZHANG,G.CORONADO,Z.HUANG JRNL TITL DNA OCTAMER D (GTSEGTACAC) PARTIALLY CROSSLINKED WITH JRNL TITL 2 PLATINUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 4265 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 206 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) : 1.42 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 293 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.4020 REMARK 3 BIN FREE R VALUE SET COUNT : 20 REMARK 3 BIN FREE R VALUE : 0.4570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 163 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) : 19.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.03000 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): 0.074 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.074 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.458 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 180 ; 0.027 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 271 ; 3.145 ; 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 ; 0.437 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 84 ; 0.029 ; 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): 180 ; 2.456 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 271 ; 3.151 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4H5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000075036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 99 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 5 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4265 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 21.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.58400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.730 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PLATINUM WAS ADDED TO THE REMARK 280 CRYSTALLIZATION BUFFER , PH 6.8, VAPOR DIFFUSION, HANGING 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 12.15500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.15500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.15500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.23250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.15500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.15500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 6.07750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.15500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.15500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 18.23250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.15500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.15500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 6.07750 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 12.15500 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: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 -12.15500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 234 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 209 O HOH A 223 1.79 REMARK 500 OP2 DG A 3 O HOH A 231 1.94 REMARK 500 O HOH A 222 O HOH A 223 2.00 REMARK 500 O HOH A 227 O HOH A 231 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 224 O HOH A 232 7655 1.98 REMARK 500 REMARK 500 REMARK: NULL 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 2ST A 2 O3' DG A 3 P 0.160 REMARK 500 DG A 3 C5 DG A 3 N7 0.044 REMARK 500 DC A 8 N3 DC A 8 C4 -0.043 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 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES REMARK 500 DG A 3 C4' - C3' - C2' ANGL. DEV. = -10.3 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG A 3 N3 - C4 - C5 ANGL. DEV. = 5.4 DEGREES REMARK 500 DG A 3 C5 - N7 - C8 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 3 N3 - C4 - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG A 4 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES REMARK 500 DC A 5 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 6 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 DC A 6 N3 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 6 N3 - C2 - O2 ANGL. DEV. = 5.2 DEGREES REMARK 500 DA A 7 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DA A 7 C6 - N1 - C2 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 7 N1 - C2 - N3 ANGL. DEV. = -4.0 DEGREES REMARK 500 DA A 7 N9 - C4 - C5 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA A 7 N1 - C6 - N6 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC A 8 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 DC A 8 N1 - C2 - N3 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC A 8 C2 - N3 - C4 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC A 8 N3 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PT A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FP6 RELATED DB: PDB REMARK 900 SE-DNA WITHOUT PLATINUM CROSSLINKED DBREF 4H5A A 1 8 PDB 4H5A 4H5A 1 8 SEQRES 1 A 8 DG 2ST DG DG DC DC DA DC MODRES 4H5A 2ST A 2 DT HET 2ST A 2 22 HET PT A 101 1 HETNAM 2ST 5-METHYL-2'-SE-METHYL-2'-SELENOURIDINE 5'-(DIHYDROGEN HETNAM 2 2ST PHOSPHATE) HETNAM PT PLATINUM (II) ION FORMUL 1 2ST C11 H17 N2 O8 P SE FORMUL 2 PT PT 2+ FORMUL 3 HOH *36(H2 O) LINK O3' DG A 1 P 2ST A 2 1555 1555 1.63 LINK O3' 2ST A 2 P DG A 3 1555 1555 1.77 LINK N7 DG A 4 PT PT A 101 1555 1555 2.18 SITE 1 AC1 2 DG A 4 HOH A 220 CRYST1 42.310 42.310 24.310 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 0.023635 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.041135 0.00000 ATOM 1 O5' DG A 1 -2.253 -7.530 -11.411 1.00 18.64 O ATOM 2 C5' DG A 1 -3.671 -7.405 -11.048 1.00 17.67 C ATOM 3 C4' DG A 1 -4.176 -8.637 -10.329 1.00 15.92 C ATOM 4 O4' DG A 1 -4.077 -9.799 -11.220 1.00 16.24 O ATOM 5 C3' DG A 1 -3.446 -9.050 -9.073 1.00 16.79 C ATOM 6 O3' DG A 1 -3.944 -8.250 -7.942 1.00 19.82 O ATOM 7 C2' DG A 1 -3.798 -10.543 -8.970 1.00 15.57 C ATOM 8 C1' DG A 1 -3.725 -10.916 -10.432 1.00 15.17 C ATOM 9 N9 DG A 1 -2.369 -11.305 -10.841 1.00 14.24 N ATOM 10 C8 DG A 1 -1.484 -10.578 -11.591 1.00 13.68 C ATOM 11 N7 DG A 1 -0.343 -11.231 -11.780 1.00 14.79 N ATOM 12 C5 DG A 1 -0.502 -12.432 -11.113 1.00 13.04 C ATOM 13 C6 DG A 1 0.415 -13.526 -10.962 1.00 13.14 C ATOM 14 O6 DG A 1 1.548 -13.654 -11.492 1.00 15.85 O ATOM 15 N1 DG A 1 -0.182 -14.547 -10.231 1.00 13.81 N ATOM 16 C2 DG A 1 -1.396 -14.541 -9.650 1.00 16.75 C ATOM 17 N2 DG A 1 -1.783 -15.599 -8.972 1.00 17.67 N ATOM 18 N3 DG A 1 -2.253 -13.538 -9.775 1.00 16.28 N ATOM 19 C4 DG A 1 -1.729 -12.490 -10.485 1.00 14.45 C HETATM 20 P 2ST A 2 -2.950 -7.826 -6.728 1.00 20.21 P HETATM 21 OP1 2ST A 2 -3.922 -6.890 -5.861 1.00 22.79 O HETATM 22 OP2 2ST A 2 -1.622 -7.326 -7.297 1.00 18.27 O HETATM 23 O5' 2ST A 2 -2.702 -9.281 -5.998 1.00 18.81 O HETATM 24 N1 2ST A 2 -0.718 -12.642 -6.468 1.00 16.29 N HETATM 25 C6 2ST A 2 -0.531 -11.455 -7.099 1.00 15.65 C HETATM 26 C2 2ST A 2 0.222 -13.603 -6.612 1.00 17.61 C HETATM 27 O2 2ST A 2 0.123 -14.685 -5.980 1.00 18.94 O HETATM 28 N3 2ST A 2 1.287 -13.362 -7.388 1.00 14.89 N HETATM 29 C4 2ST A 2 1.526 -12.176 -8.044 1.00 13.65 C HETATM 30 O4 2ST A 2 2.500 -12.022 -8.780 1.00 14.73 O HETATM 31 C5 2ST A 2 0.526 -11.135 -7.921 1.00 14.60 C HETATM 32 C5A 2ST A 2 0.716 -9.816 -8.618 1.00 15.06 C HETATM 33 C2' 2ST A 2 -1.603 -12.753 -4.141 1.00 19.68 C HETATM 34 C5' 2ST A 2 -3.737 -9.873 -5.283 1.00 18.51 C HETATM 35 C4' 2ST A 2 -3.262 -11.248 -4.851 1.00 18.19 C HETATM 36 O4' 2ST A 2 -2.893 -12.046 -5.981 1.00 16.85 O HETATM 37 C1' 2ST A 2 -1.874 -12.937 -5.624 1.00 17.83 C HETATM 38 C3' 2ST A 2 -1.994 -11.286 -4.003 1.00 20.61 C HETATM 39 SE 2ST A 2 -2.750 -13.933 -3.001 1.00 25.26 SE HETATM 40 CA' 2ST A 2 -1.750 -15.605 -3.339 1.00 23.17 C HETATM 41 O3' 2ST A 2 -2.313 -10.905 -2.689 1.00 25.73 O ATOM 42 P DG A 3 -1.043 -10.054 -1.803 1.00 28.71 P ATOM 43 OP1 DG A 3 -1.761 -9.636 -0.625 1.00 34.75 O ATOM 44 OP2 DG A 3 -0.373 -9.059 -2.677 1.00 30.44 O ATOM 45 O5' DG A 3 0.160 -11.081 -1.483 1.00 28.51 O ATOM 46 C5' DG A 3 -0.071 -12.247 -0.768 1.00 27.98 C ATOM 47 C4' DG A 3 1.084 -13.229 -0.950 1.00 23.53 C ATOM 48 O4' DG A 3 0.985 -13.676 -2.334 1.00 21.19 O ATOM 49 C3' DG A 3 2.558 -12.828 -0.789 1.00 23.77 C ATOM 50 O3' DG A 3 2.962 -12.754 0.626 1.00 22.65 O ATOM 51 C2' DG A 3 3.034 -14.117 -1.460 1.00 20.91 C ATOM 52 C1' DG A 3 2.215 -14.206 -2.749 1.00 21.18 C ATOM 53 N9 DG A 3 2.797 -13.386 -3.829 1.00 18.68 N ATOM 54 C8 DG A 3 2.469 -12.144 -4.269 1.00 18.09 C ATOM 55 N7 DG A 3 3.175 -11.638 -5.224 1.00 20.22 N ATOM 56 C5 DG A 3 4.121 -12.694 -5.426 1.00 16.64 C ATOM 57 C6 DG A 3 5.234 -12.823 -6.321 1.00 13.81 C ATOM 58 O6 DG A 3 5.597 -12.038 -7.165 1.00 16.57 O ATOM 59 N1 DG A 3 5.898 -14.069 -6.119 1.00 15.67 N ATOM 60 C2 DG A 3 5.560 -15.055 -5.240 1.00 13.58 C ATOM 61 N2 DG A 3 6.348 -16.141 -5.230 1.00 15.86 N ATOM 62 N3 DG A 3 4.542 -14.947 -4.403 1.00 16.17 N ATOM 63 C4 DG A 3 3.911 -13.762 -4.593 1.00 15.87 C ATOM 64 P DG A 4 4.266 -11.959 1.103 1.00 23.47 P ATOM 65 OP1 DG A 4 4.275 -12.098 2.600 1.00 28.49 O ATOM 66 OP2 DG A 4 4.478 -10.688 0.436 1.00 26.81 O ATOM 67 O5' DG A 4 5.435 -12.917 0.554 1.00 23.00 O ATOM 68 C5' DG A 4 5.543 -14.234 1.057 1.00 21.76 C ATOM 69 C4' DG A 4 6.667 -14.989 0.325 1.00 21.55 C ATOM 70 O4' DG A 4 6.431 -15.004 -1.125 1.00 18.63 O ATOM 71 C3' DG A 4 7.977 -14.290 0.373 1.00 21.16 C ATOM 72 O3' DG A 4 8.546 -14.687 1.617 1.00 23.43 O ATOM 73 C2' DG A 4 8.729 -14.899 -0.788 1.00 18.33 C ATOM 74 C1' DG A 4 7.643 -14.898 -1.866 1.00 16.65 C ATOM 75 N9 DG A 4 7.529 -13.665 -2.650 1.00 17.31 N ATOM 76 C8 DG A 4 6.644 -12.610 -2.477 1.00 17.92 C ATOM 77 N7 DG A 4 6.804 -11.641 -3.339 1.00 15.96 N ATOM 78 C5 DG A 4 7.819 -12.140 -4.153 1.00 13.93 C ATOM 79 C6 DG A 4 8.419 -11.571 -5.327 1.00 13.39 C ATOM 80 O6 DG A 4 8.149 -10.493 -5.908 1.00 16.52 O ATOM 81 N1 DG A 4 9.422 -12.401 -5.841 1.00 11.84 N ATOM 82 C2 DG A 4 9.812 -13.602 -5.271 1.00 11.88 C ATOM 83 N2 DG A 4 10.822 -14.254 -5.831 1.00 13.72 N ATOM 84 N3 DG A 4 9.249 -14.130 -4.223 1.00 12.19 N ATOM 85 C4 DG A 4 8.263 -13.383 -3.719 1.00 13.98 C ATOM 86 P DC A 5 9.480 -13.758 2.473 1.00 24.72 P ATOM 87 OP1 DC A 5 9.516 -14.387 3.788 1.00 27.28 O ATOM 88 OP2 DC A 5 9.344 -12.386 2.208 1.00 21.44 O ATOM 89 O5' DC A 5 10.907 -14.202 1.890 1.00 27.80 O ATOM 90 C5' DC A 5 11.984 -13.427 1.719 1.00 22.28 C ATOM 91 C4' DC A 5 12.741 -14.065 0.575 1.00 19.64 C ATOM 92 O4' DC A 5 11.870 -14.174 -0.619 1.00 16.88 O ATOM 93 C3' DC A 5 13.858 -13.129 0.196 1.00 18.20 C ATOM 94 O3' DC A 5 14.985 -13.478 0.947 1.00 18.61 O ATOM 95 C2' DC A 5 13.980 -13.370 -1.270 1.00 16.15 C ATOM 96 C1' DC A 5 12.550 -13.579 -1.733 1.00 16.34 C ATOM 97 N1 DC A 5 11.836 -12.360 -2.161 1.00 15.07 N ATOM 98 C2 DC A 5 12.150 -11.769 -3.370 1.00 12.85 C ATOM 99 O2 DC A 5 13.051 -12.208 -4.053 1.00 14.03 O ATOM 100 N3 DC A 5 11.541 -10.670 -3.806 1.00 13.43 N ATOM 101 C4 DC A 5 10.551 -10.159 -3.048 1.00 14.38 C ATOM 102 N4 DC A 5 9.911 -9.101 -3.533 1.00 15.22 N ATOM 103 C5 DC A 5 10.166 -10.699 -1.783 1.00 14.98 C ATOM 104 C6 DC A 5 10.845 -11.789 -1.366 1.00 17.36 C ATOM 105 P DC A 6 16.028 -12.334 1.398 1.00 19.76 P ATOM 106 OP1 DC A 6 17.032 -13.099 2.175 1.00 22.40 O ATOM 107 OP2 DC A 6 15.283 -11.242 1.927 1.00 20.83 O ATOM 108 O5' DC A 6 16.735 -11.838 0.083 1.00 16.99 O ATOM 109 C5' DC A 6 17.611 -12.648 -0.617 1.00 17.18 C ATOM 110 C4' DC A 6 18.024 -11.970 -1.906 1.00 16.50 C ATOM 111 O4' DC A 6 16.913 -11.832 -2.801 1.00 16.80 O ATOM 112 C3' DC A 6 18.529 -10.546 -1.805 1.00 16.41 C ATOM 113 O3' DC A 6 19.885 -10.511 -1.315 1.00 18.26 O ATOM 114 C2' DC A 6 18.375 -10.050 -3.242 1.00 15.73 C ATOM 115 C1' DC A 6 17.046 -10.660 -3.619 1.00 14.21 C ATOM 116 N1 DC A 6 15.902 -9.725 -3.339 1.00 12.98 N ATOM 117 C2 DC A 6 15.634 -8.713 -4.297 1.00 11.92 C ATOM 118 O2 DC A 6 16.439 -8.626 -5.230 1.00 14.74 O ATOM 119 N3 DC A 6 14.506 -7.927 -4.087 1.00 12.43 N ATOM 120 C4 DC A 6 13.708 -8.112 -3.007 1.00 12.11 C ATOM 121 N4 DC A 6 12.629 -7.353 -2.849 1.00 15.50 N ATOM 122 C5 DC A 6 14.039 -9.148 -2.048 1.00 12.48 C ATOM 123 C6 DC A 6 15.116 -9.894 -2.253 1.00 13.96 C ATOM 124 P DA A 7 20.452 -9.260 -0.503 1.00 17.56 P ATOM 125 OP1 DA A 7 21.791 -9.702 0.009 1.00 21.80 O ATOM 126 OP2 DA A 7 19.483 -8.680 0.409 1.00 17.88 O ATOM 127 O5' DA A 7 20.636 -8.201 -1.634 1.00 15.68 O ATOM 128 C5' DA A 7 21.536 -8.425 -2.699 1.00 16.09 C ATOM 129 C4' DA A 7 21.476 -7.283 -3.677 1.00 17.16 C ATOM 130 O4' DA A 7 20.156 -7.243 -4.276 1.00 16.39 O ATOM 131 C3' DA A 7 21.598 -5.880 -3.117 1.00 14.76 C ATOM 132 O3' DA A 7 23.032 -5.554 -3.027 1.00 18.43 O ATOM 133 C2' DA A 7 20.913 -4.990 -4.129 1.00 12.64 C ATOM 134 C1' DA A 7 19.740 -5.883 -4.499 1.00 14.62 C ATOM 135 N9 DA A 7 18.480 -5.703 -3.744 1.00 12.30 N ATOM 136 C8 DA A 7 18.007 -6.410 -2.694 1.00 13.00 C ATOM 137 N7 DA A 7 16.818 -6.037 -2.319 1.00 12.31 N ATOM 138 C5 DA A 7 16.485 -4.989 -3.196 1.00 12.56 C ATOM 139 C6 DA A 7 15.330 -4.184 -3.367 1.00 13.03 C ATOM 140 N6 DA A 7 14.251 -4.336 -2.593 1.00 12.49 N ATOM 141 N1 DA A 7 15.393 -3.273 -4.392 1.00 13.95 N ATOM 142 C2 DA A 7 16.471 -3.142 -5.184 1.00 12.16 C ATOM 143 N3 DA A 7 17.566 -3.880 -5.114 1.00 12.42 N ATOM 144 C4 DA A 7 17.485 -4.803 -4.149 1.00 12.68 C ATOM 145 P DC A 8 23.549 -4.542 -1.924 1.00 19.74 P ATOM 146 OP1 DC A 8 25.020 -4.604 -2.154 1.00 22.28 O ATOM 147 OP2 DC A 8 23.012 -4.969 -0.647 1.00 24.39 O ATOM 148 O5' DC A 8 22.979 -3.162 -2.299 1.00 17.68 O ATOM 149 C5' DC A 8 23.420 -2.477 -3.419 1.00 17.10 C ATOM 150 C4' DC A 8 22.670 -1.204 -3.755 1.00 17.81 C ATOM 151 O4' DC A 8 21.267 -1.544 -3.792 1.00 19.48 O ATOM 152 C3' DC A 8 22.827 -0.192 -2.625 1.00 20.44 C ATOM 153 O3' DC A 8 23.067 1.026 -3.314 1.00 28.03 O ATOM 154 C2' DC A 8 21.526 -0.124 -1.839 1.00 20.76 C ATOM 155 C1' DC A 8 20.575 -0.611 -2.964 1.00 19.03 C ATOM 156 N1 DC A 8 19.393 -1.258 -2.373 1.00 15.37 N ATOM 157 C2 DC A 8 18.065 -0.798 -2.655 1.00 15.49 C ATOM 158 O2 DC A 8 17.868 0.136 -3.417 1.00 19.58 O ATOM 159 N3 DC A 8 17.113 -1.459 -1.921 1.00 12.05 N ATOM 160 C4 DC A 8 17.337 -2.456 -1.131 1.00 2.00 C ATOM 161 N4 DC A 8 16.300 -2.932 -0.521 1.00 12.63 N ATOM 162 C5 DC A 8 18.605 -2.976 -0.935 1.00 11.52 C ATOM 163 C6 DC A 8 19.633 -2.342 -1.611 1.00 14.50 C TER 164 DC A 8 HETATM 165 PT PT A 101 5.804 -9.715 -3.190 0.25 33.95 PT HETATM 166 O HOH A 201 -0.901 -6.150 -9.464 1.00 25.46 O HETATM 167 O HOH A 202 1.676 -10.141 -12.830 1.00 19.33 O HETATM 168 O HOH A 203 14.751 -14.322 -4.753 1.00 17.61 O HETATM 169 O HOH A 204 -0.314 -17.352 -6.039 1.00 23.66 O HETATM 170 O HOH A 205 -4.882 -4.603 -6.886 1.00 25.80 O HETATM 171 O HOH A 206 19.877 -2.557 -6.263 1.00 22.00 O HETATM 172 O HOH A 207 19.282 -5.919 0.964 1.00 25.89 O HETATM 173 O HOH A 208 16.934 -15.418 -3.390 1.00 25.24 O HETATM 174 O HOH A 209 15.305 -6.498 -0.021 1.00 24.46 O HETATM 175 O HOH A 210 13.241 -5.636 -0.047 1.00 26.41 O HETATM 176 O HOH A 211 25.416 -0.047 -5.110 1.00 25.73 O HETATM 177 O HOH A 212 5.815 -9.217 -6.808 1.00 25.84 O HETATM 178 O HOH A 213 26.086 -4.349 -4.534 1.00 22.41 O HETATM 179 O HOH A 214 -1.783 -7.005 -14.025 1.00 31.03 O HETATM 180 O HOH A 215 -2.968 -5.315 -19.425 1.00 33.77 O HETATM 181 O HOH A 216 0.325 -18.360 -1.395 1.00 28.56 O HETATM 182 O HOH A 217 1.587 -18.105 -3.897 1.00 25.72 O HETATM 183 O HOH A 218 4.198 -16.955 -2.673 1.00 27.95 O HETATM 184 O HOH A 219 4.437 -17.668 0.098 1.00 33.33 O HETATM 185 O HOH A 220 7.806 -7.853 -2.257 1.00 37.21 O HETATM 186 O HOH A 221 11.163 -7.527 -0.397 1.00 24.89 O HETATM 187 O HOH A 222 16.939 -8.790 1.475 1.00 34.13 O HETATM 188 O HOH A 223 16.714 -7.593 -0.116 1.00 33.02 O HETATM 189 O HOH A 224 26.564 -1.914 -0.788 1.00 38.21 O HETATM 190 O HOH A 225 -3.862 -3.504 -11.058 1.00 40.22 O HETATM 191 O HOH A 226 3.246 -9.013 -6.104 1.00 29.57 O HETATM 192 O HOH A 227 0.569 -7.796 -5.493 1.00 31.10 O HETATM 193 O HOH A 228 -4.385 -6.713 -3.237 1.00 36.31 O HETATM 194 O HOH A 229 3.401 -12.187 -12.857 1.00 29.61 O HETATM 195 O HOH A 230 -3.766 -12.673 1.267 1.00 41.79 O HETATM 196 O HOH A 231 1.044 -9.203 -3.990 1.00 49.38 O HETATM 197 O HOH A 232 -0.153 -16.536 0.357 1.00 51.57 O HETATM 198 O HOH A 233 9.947 -4.497 -2.624 1.00 35.80 O HETATM 199 O HOH A 234 9.264 -9.264 6.078 0.50 33.07 O HETATM 200 O HOH A 235 7.183 -7.615 -5.563 0.50 32.56 O HETATM 201 O HOH A 236 2.929 -8.722 -2.091 1.00 38.58 O CONECT 6 20 CONECT 20 6 21 22 23 CONECT 21 20 CONECT 22 20 CONECT 23 20 34 CONECT 24 25 26 37 CONECT 25 24 31 CONECT 26 24 27 28 CONECT 27 26 CONECT 28 26 29 CONECT 29 28 30 31 CONECT 30 29 CONECT 31 25 29 32 CONECT 32 31 CONECT 33 37 38 39 CONECT 34 23 35 CONECT 35 34 36 38 CONECT 36 35 37 CONECT 37 24 33 36 CONECT 38 33 35 41 CONECT 39 33 40 CONECT 40 39 CONECT 41 38 42 CONECT 42 41 CONECT 77 165 CONECT 165 77 MASTER 368 0 2 0 0 0 1 6 200 1 26 1 END