HEADER DNA 07-JUN-10 3AJK TITLE CRYSTAL STRUCTURE OF D(CGCGGATF5UCGCG): 5-FORMYLURIDINE:GUANOSINE TITLE 2 BASE-PAIR IN B-DNA WITH HOECHST33258 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*GP*AP*TP*(UFR)P*CP*GP*CP*G*)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC DNA KEYWDS DOUBLE HELIX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.TSUNODA,T.SAKAUE,Y.UENO,A.MATSUDA,A.TAKENAKA REVDAT 2 01-NOV-23 3AJK 1 REMARK LINK REVDAT 1 27-APR-11 3AJK 0 JRNL AUTH M.TSUNODA,T.SAKAUE,S.NAITO,T.SUNAMI,N.ABE,Y.UENO,A.MATSUDA, JRNL AUTH 2 A.TAKENAKA JRNL TITL INSIGHTS INTO THE STRUCTURES OF DNA DAMAGED BY HYDROXYL JRNL TITL 2 RADICAL: CRYSTAL STRUCTURES OF DNA DUPLEXES CONTAINING JRNL TITL 3 5-FORMYLURACIL JRNL REF J NUCLEIC ACIDS V.2010 07289 2010 JRNL REFN ISSN 2090-0201 JRNL PMID 20976303 JRNL DOI 10.4061/2010/107289 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 4716 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 513 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 325 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.4050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 490 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.42000 REMARK 3 B22 (A**2) : -0.77000 REMARK 3 B33 (A**2) : -1.65000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.195 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.133 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.704 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 587 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 898 ; 3.096 ; 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): 96 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 284 ; 0.017 ; 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): 587 ; 2.956 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 898 ; 4.065 ; 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 3AJK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000029330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-01 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DPS REMARK 200 DATA SCALING SOFTWARE : DPS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5312 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 34.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33100 REMARK 200 R SYM FOR SHELL (I) : 0.30600 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 355D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM NA CACODYLATE, 0.5MM SPERMINE, REMARK 280 40MM NACL, 10MM MGCL2, 5% MPD, 0.5MM HOECHST33258, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 12.66350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.98050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.16550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.98050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.66350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.16550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 O5 UFR A 8 O HOH A 1120 2.01 REMARK 500 OP2 DG A 12 O HOH A 1058 2.10 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 DG A 5 C2 DG A 5 N3 0.052 REMARK 500 DG A 10 O4' DG A 10 C4' 0.065 REMARK 500 DG A 10 O3' DG A 10 C3' -0.050 REMARK 500 DC B 13 O3' DC B 13 C3' -0.070 REMARK 500 DC B 15 O3' DC B 15 C3' -0.044 REMARK 500 DG B 16 N3 DG B 16 C4 0.053 REMARK 500 DG B 16 C5 DG B 16 N7 0.049 REMARK 500 DT B 19 O3' DT B 19 C3' -0.036 REMARK 500 DC B 21 N1 DC B 21 C6 0.044 REMARK 500 DG B 22 O3' DG B 22 C3' -0.071 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 DC A 1 O5' - C5' - C4' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -2.8 DEGREES REMARK 500 DG A 2 C2 - N3 - C4 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC A 3 N3 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 4 O4' - C1' - C2' ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 7.9 DEGREES REMARK 500 DG A 5 O5' - C5' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA A 6 OP1 - P - OP2 ANGL. DEV. = 9.6 DEGREES REMARK 500 DA A 6 O5' - P - OP2 ANGL. DEV. = -5.7 DEGREES REMARK 500 DA A 6 O5' - C5' - C4' ANGL. DEV. = -5.4 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = -6.9 DEGREES REMARK 500 DT A 7 OP1 - P - OP2 ANGL. DEV. = 9.3 DEGREES REMARK 500 DT A 7 O5' - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG A 12 N1 - C6 - O6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 12 C5 - C6 - O6 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC B 13 C3' - C2' - C1' ANGL. DEV. = -6.8 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 13 C6 - N1 - C2 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 DG B 14 N1 - C6 - O6 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 14 C5 - C6 - O6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG B 16 OP1 - P - OP2 ANGL. DEV. = 9.3 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 17 C5 - C6 - O6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT B 19 OP1 - P - OP2 ANGL. DEV. = 9.9 DEGREES REMARK 500 DT B 19 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = -10.8 DEGREES REMARK 500 DC B 23 O4' - C1' - N1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC B 23 N3 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 23 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG B 24 O5' - C5' - C4' ANGL. DEV. = -6.3 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 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1003 O REMARK 620 2 HOH A1009 O 86.8 REMARK 620 3 HOH A1010 O 174.3 89.9 REMARK 620 4 HOH A1016 O 82.1 168.9 101.2 REMARK 620 5 HOH A1050 O 85.4 89.1 90.0 89.5 REMARK 620 6 HOH A1060 O 88.3 83.8 95.9 96.4 170.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HT A 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AJJ RELATED DB: PDB REMARK 900 THE SAME DNA WITHOUT DRUG. REMARK 900 RELATED ID: 3AJL RELATED DB: PDB REMARK 900 THE SAME DNA WITH DAPI DBREF 3AJK A 1 12 PDB 3AJK 3AJK 1 12 DBREF 3AJK B 13 24 PDB 3AJK 3AJK 13 24 SEQRES 1 A 12 DC DG DC DG DG DA DT UFR DC DG DC DG SEQRES 1 B 12 DC DG DC DG DG DA DT UFR DC DG DC DG MODRES 3AJK UFR A 8 DU MODRES 3AJK UFR B 20 DU HET UFR A 8 21 HET UFR B 20 22 HET HT A 25 32 HET MG A 101 1 HETNAM UFR 2'-DEOXY-5-FORMYLURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM HT 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'- HETNAM 2 HT BI-BENZIMIDAZOLE HETNAM MG MAGNESIUM ION HETSYN HT HOECHST 33258 FORMUL 1 UFR 2(C10 H13 N2 O9 P) FORMUL 3 HT C25 H24 N6 O FORMUL 4 MG MG 2+ FORMUL 5 HOH *123(H2 O) LINK O3' DT A 7 P UFR A 8 1555 1555 1.56 LINK O3' DT B 19 P UFR B 20 1555 1555 1.63 LINK MG MG A 101 O HOH A1003 1555 1555 1.91 LINK MG MG A 101 O HOH A1009 1555 1555 2.07 LINK MG MG A 101 O HOH A1010 1555 1555 1.96 LINK MG MG A 101 O HOH A1016 1555 1555 2.20 LINK MG MG A 101 O HOH A1050 1555 1555 2.09 LINK MG MG A 101 O HOH A1060 1555 1555 2.00 SITE 1 AC1 12 DA A 6 DT A 7 UFR A 8 DC A 9 SITE 2 AC1 12 DG A 10 DC A 11 DG B 16 DA B 18 SITE 3 AC1 12 DT B 19 UFR B 20 DC B 21 DG B 24 CRYST1 25.327 40.331 65.961 90.00 90.00 90.00 P 21 21 21 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 0.039484 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024795 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015160 0.00000