HEADER DNA 30-MAR-06 2GJB TITLE CROSSLINKING OF DNA DUPLEXES: X-RAY CRYSTAL STRUCTURE OF AN TITLE 2 UNSUBSTITUTED BISACRIDINE WITH THE OLIGONUCLEOTIDE D(CGTACG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*TP*AP*CP*GP*)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA DUPLEX, BIS-INTERCALATOR, DNA EXPDTA X-RAY DIFFRACTION AUTHOR Y.GAN,C.J.CARDIN,W.A.DENNY REVDAT 5 03-APR-24 2GJB 1 REMARK REVDAT 4 14-FEB-24 2GJB 1 REMARK HETSYN LINK REVDAT 3 18-OCT-17 2GJB 1 REMARK REVDAT 2 24-FEB-09 2GJB 1 VERSN REVDAT 1 10-APR-07 2GJB 0 JRNL AUTH Y.GAN,C.J.CARDIN,W.A.DENNY JRNL TITL CROSSLINKING OF DNA DUPLEXES: X-RAY CRYSTAL STRUCTURE OF AN JRNL TITL 2 UNSUBSTITUTED BISACRIDINE WITH OLIGONUCLEOTIDE D(CGTACG) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 890 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) : 0.272 REMARK 3 R VALUE (WORKING SET) : 0.270 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 45 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 58 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3670 REMARK 3 BIN FREE R VALUE SET COUNT : 4 REMARK 3 BIN FREE R VALUE : 0.5830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 120 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.09000 REMARK 3 B22 (A**2) : 2.09000 REMARK 3 B33 (A**2) : -3.14000 REMARK 3 B12 (A**2) : 1.05000 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): 0.398 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.272 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.648 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 155 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 233 ; 3.391 ; 2.996 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): 23 ; 0.165 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 77 ; 0.017 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 27 ; 0.274 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 85 ; 0.371 ; 0.200 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): 36 ; 0.322 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.216 ; 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): 173 ; 3.483 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 233 ; 5.224 ; 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 : 1.20 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 2GJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037188. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X12 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : MOSFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1472 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 22.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 20.10 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.30 REMARK 200 R MERGE FOR SHELL (I) : 0.31200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NDB ENTRY DD0018 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE CRYSTALS GROW IN TEN DAYS FROM REMARK 280 SITTING DROPS CONTAINING 2MM DNA, 12MM SPERMINE, 80MM STRONTIUM REMARK 280 CHLORIDE, 20MM MAGNESIUM CHLORIDE, 10%MPD, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.66267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.33133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.49700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 13.16567 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 65.82833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.66267 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 26.33133 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 13.16567 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 39.49700 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 65.82833 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS 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 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 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 13.16567 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 N17 BMO A 8 LIES ON A SPECIAL POSITION. 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 3 O3' DT A 3 C3' -0.068 REMARK 500 DT A 3 C1' DT A 3 N1 0.097 REMARK 500 DC A 5 C2 DC A 5 N3 -0.048 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 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 14.8 DEGREES REMARK 500 DT A 3 O3' - P - O5' ANGL. DEV. = -17.6 DEGREES REMARK 500 DT A 3 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 DT A 3 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 3 N1 - C2 - O2 ANGL. DEV. = 6.2 DEGREES REMARK 500 DT A 3 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 4 O5' - P - OP2 ANGL. DEV. = 7.5 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = -7.9 DEGREES REMARK 500 DC A 5 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC A 5 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC A 5 C6 - N1 - C2 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC A 5 N3 - C4 - N4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG A 6 O4' - C4' - C3' ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG A 6 N3 - C2 - N2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 6 N1 - C6 - O6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 6 C5 - C6 - O6 ANGL. DEV. = -4.5 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 K A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMO A 8 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GB9 RELATED DB: PDB DBREF 2GJB A 1 6 PDB 2GJB 2GJB 1 6 SEQRES 1 A 6 DC DG DT DA DC DG HET K A 7 1 HET BMO A 8 19 HETNAM K POTASSIUM ION HETNAM BMO N-ACRIDIN-9-YL-N'-[3-(ACRIDIN-9-YLAMINO)PROPYL]PROPANE- HETNAM 2 BMO 1,3-DIAMINE HETSYN BMO 1,3-PROPANEDIAMINE; N-9-ACRIDINYL-N -[3-(9- HETSYN 2 BMO ACRIDINYLAMINO)PROPYL] FORMUL 2 K K 1+ FORMUL 3 BMO C32 H31 N5 FORMUL 4 HOH *(H2 O) LINK N17 BMO A 8 C19 BMO A 8 1555 11655 1.61 LINK O4 DT A 3 K K A 7 10555 1555 2.87 SITE 1 AC1 1 DT A 3 SITE 1 AC2 4 DC A 1 DG A 2 DC A 5 DG A 6 CRYST1 25.750 25.750 78.994 90.00 90.00 120.00 P 65 2 2 12 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 0.038835 0.022421 0.000000 0.00000 SCALE2 0.000000 0.044842 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012659 0.00000 ATOM 1 O5' DC A 1 15.551 -17.223 15.736 1.00 67.53 O ATOM 2 C5' DC A 1 14.337 -16.994 16.495 1.00 65.05 C ATOM 3 C4' DC A 1 13.196 -16.590 15.560 1.00 62.49 C ATOM 4 O4' DC A 1 12.315 -15.571 16.132 1.00 59.71 O ATOM 5 C3' DC A 1 13.647 -16.103 14.183 1.00 61.50 C ATOM 6 O3' DC A 1 12.962 -16.926 13.242 1.00 58.84 O ATOM 7 C2' DC A 1 13.294 -14.598 14.162 1.00 60.34 C ATOM 8 C1' DC A 1 12.274 -14.431 15.304 1.00 56.22 C ATOM 9 N1 DC A 1 12.384 -13.160 16.166 1.00 52.95 N ATOM 10 C2 DC A 1 11.189 -12.569 16.641 1.00 46.16 C ATOM 11 O2 DC A 1 10.100 -13.077 16.401 1.00 43.26 O ATOM 12 N3 DC A 1 11.260 -11.478 17.414 1.00 49.20 N ATOM 13 C4 DC A 1 12.429 -10.905 17.682 1.00 50.81 C ATOM 14 N4 DC A 1 12.402 -9.800 18.434 1.00 50.56 N ATOM 15 C5 DC A 1 13.670 -11.490 17.241 1.00 52.22 C ATOM 16 C6 DC A 1 13.597 -12.600 16.486 1.00 50.36 C ATOM 17 P DG A 2 13.106 -16.775 11.668 1.00 59.52 P ATOM 18 OP1 DG A 2 12.705 -18.031 10.988 1.00 59.27 O ATOM 19 OP2 DG A 2 14.414 -16.115 11.313 1.00 57.15 O ATOM 20 O5' DG A 2 11.860 -15.786 11.515 1.00 60.07 O ATOM 21 C5' DG A 2 10.537 -16.354 11.207 1.00 55.99 C ATOM 22 C4' DG A 2 9.850 -15.535 10.137 1.00 52.56 C ATOM 23 O4' DG A 2 9.945 -14.163 10.613 1.00 49.23 O ATOM 24 C3' DG A 2 10.398 -15.551 8.684 1.00 53.88 C ATOM 25 O3' DG A 2 9.443 -15.074 7.790 1.00 57.06 O ATOM 26 C2' DG A 2 11.379 -14.398 8.774 1.00 50.04 C ATOM 27 C1' DG A 2 10.485 -13.417 9.534 1.00 46.91 C ATOM 28 N9 DG A 2 11.170 -12.198 9.981 1.00 41.75 N ATOM 29 C8 DG A 2 12.514 -12.046 10.139 1.00 40.94 C ATOM 30 N7 DG A 2 12.865 -10.858 10.520 1.00 44.50 N ATOM 31 C5 DG A 2 11.663 -10.158 10.571 1.00 40.22 C ATOM 32 C6 DG A 2 11.435 -8.798 10.907 1.00 38.06 C ATOM 33 O6 DG A 2 12.283 -7.943 11.244 1.00 43.18 O ATOM 34 N1 DG A 2 10.071 -8.492 10.892 1.00 32.84 N ATOM 35 C2 DG A 2 9.104 -9.366 10.495 1.00 32.79 C ATOM 36 N2 DG A 2 7.887 -8.876 10.522 1.00 34.56 N ATOM 37 N3 DG A 2 9.283 -10.657 10.168 1.00 32.84 N ATOM 38 C4 DG A 2 10.603 -10.977 10.245 1.00 38.27 C ATOM 39 P DT A 3 8.919 -15.544 6.321 1.00 58.99 P ATOM 40 OP1 DT A 3 8.548 -16.992 6.288 1.00 61.00 O ATOM 41 OP2 DT A 3 9.651 -14.863 5.223 1.00 51.95 O ATOM 42 O5' DT A 3 7.566 -14.794 6.675 1.00 51.99 O ATOM 43 C5' DT A 3 6.473 -14.746 5.909 1.00 48.22 C ATOM 44 C4' DT A 3 6.077 -13.298 5.922 1.00 42.63 C ATOM 45 O4' DT A 3 7.032 -12.413 6.629 1.00 38.38 O ATOM 46 C3' DT A 3 6.051 -12.834 4.517 1.00 42.12 C ATOM 47 O3' DT A 3 4.785 -12.366 4.449 1.00 41.09 O ATOM 48 C2' DT A 3 7.089 -11.665 4.512 1.00 39.97 C ATOM 49 C1' DT A 3 7.150 -11.200 5.952 1.00 34.02 C ATOM 50 N1 DT A 3 8.524 -10.535 6.380 1.00 32.46 N ATOM 51 C2 DT A 3 8.581 -9.236 6.821 1.00 27.55 C ATOM 52 O2 DT A 3 7.653 -8.400 6.956 1.00 28.79 O ATOM 53 N3 DT A 3 9.845 -8.852 7.111 1.00 33.16 N ATOM 54 C4 DT A 3 11.022 -9.552 7.027 1.00 32.89 C ATOM 55 O4 DT A 3 12.071 -9.061 7.392 1.00 35.21 O ATOM 56 C5 DT A 3 10.921 -10.910 6.571 1.00 37.69 C ATOM 57 C7 DT A 3 12.186 -11.578 6.093 1.00 35.97 C ATOM 58 C6 DT A 3 9.676 -11.323 6.268 1.00 34.25 C ATOM 59 P DA A 4 4.229 -11.875 3.073 1.00 44.99 P ATOM 60 OP1 DA A 4 2.755 -12.136 3.081 1.00 49.69 O ATOM 61 OP2 DA A 4 5.140 -12.625 2.151 1.00 47.23 O ATOM 62 O5' DA A 4 4.278 -10.292 3.050 1.00 45.33 O ATOM 63 C5' DA A 4 3.562 -9.635 4.056 1.00 42.09 C ATOM 64 C4' DA A 4 3.824 -8.161 3.889 1.00 46.55 C ATOM 65 O4' DA A 4 5.225 -7.929 4.184 1.00 42.48 O ATOM 66 C3' DA A 4 3.659 -7.787 2.438 1.00 46.77 C ATOM 67 O3' DA A 4 2.922 -6.577 2.410 1.00 48.66 O ATOM 68 C2' DA A 4 5.115 -7.622 1.912 1.00 41.93 C ATOM 69 C1' DA A 4 5.784 -7.093 3.160 1.00 38.13 C ATOM 70 N9 DA A 4 7.215 -7.411 3.319 1.00 34.69 N ATOM 71 C8 DA A 4 7.801 -8.619 3.037 1.00 35.93 C ATOM 72 N7 DA A 4 9.067 -8.730 3.366 1.00 34.03 N ATOM 73 C5 DA A 4 9.318 -7.464 3.892 1.00 31.20 C ATOM 74 C6 DA A 4 10.512 -6.889 4.370 1.00 29.38 C ATOM 75 N6 DA A 4 11.680 -7.577 4.472 1.00 30.91 N ATOM 76 N1 DA A 4 10.431 -5.634 4.845 1.00 25.81 N ATOM 77 C2 DA A 4 9.240 -4.984 4.803 1.00 25.68 C ATOM 78 N3 DA A 4 8.065 -5.421 4.360 1.00 30.09 N ATOM 79 C4 DA A 4 8.166 -6.681 3.927 1.00 29.09 C ATOM 80 P DC A 5 2.359 -6.184 0.983 1.00 48.44 P ATOM 81 OP1 DC A 5 1.057 -5.516 1.234 1.00 50.29 O ATOM 82 OP2 DC A 5 2.520 -7.303 0.098 1.00 39.98 O ATOM 83 O5' DC A 5 3.301 -5.010 0.456 1.00 51.26 O ATOM 84 C5' DC A 5 3.197 -3.688 0.998 1.00 49.29 C ATOM 85 C4' DC A 5 4.471 -2.927 0.672 1.00 45.62 C ATOM 86 O4' DC A 5 5.492 -3.814 1.168 1.00 43.48 O ATOM 87 C3' DC A 5 4.741 -2.688 -0.808 1.00 46.73 C ATOM 88 O3' DC A 5 4.496 -1.344 -1.310 1.00 50.02 O ATOM 89 C2' DC A 5 6.187 -3.132 -1.011 1.00 43.94 C ATOM 90 C1' DC A 5 6.601 -3.483 0.413 1.00 42.22 C ATOM 91 N1 DC A 5 7.574 -4.547 0.430 1.00 36.51 N ATOM 92 C2 DC A 5 8.802 -4.194 1.037 1.00 29.48 C ATOM 93 O2 DC A 5 8.968 -3.086 1.585 1.00 26.16 O ATOM 94 N3 DC A 5 9.735 -5.106 1.032 1.00 22.26 N ATOM 95 C4 DC A 5 9.549 -6.288 0.484 1.00 25.46 C ATOM 96 N4 DC A 5 10.616 -7.104 0.597 1.00 25.07 N ATOM 97 C5 DC A 5 8.326 -6.674 -0.141 1.00 27.58 C ATOM 98 C6 DC A 5 7.354 -5.762 -0.174 1.00 34.71 C ATOM 99 P DG A 6 4.504 -1.275 -2.883 1.00 51.52 P ATOM 100 OP1 DG A 6 3.483 -0.300 -3.327 1.00 57.19 O ATOM 101 OP2 DG A 6 4.550 -2.661 -3.373 1.00 52.81 O ATOM 102 O5' DG A 6 5.927 -0.574 -3.228 1.00 54.62 O ATOM 103 C5' DG A 6 6.150 0.819 -2.983 1.00 44.95 C ATOM 104 C4' DG A 6 7.258 1.310 -3.879 1.00 45.37 C ATOM 105 O4' DG A 6 8.469 0.547 -3.601 1.00 40.27 O ATOM 106 C3' DG A 6 7.035 0.982 -5.337 1.00 44.06 C ATOM 107 O3' DG A 6 5.998 1.722 -5.938 1.00 46.47 O ATOM 108 C2' DG A 6 8.437 1.181 -5.886 1.00 39.89 C ATOM 109 C1' DG A 6 9.266 0.575 -4.756 1.00 38.52 C ATOM 110 N9 DG A 6 9.837 -0.758 -5.025 1.00 36.33 N ATOM 111 C8 DG A 6 9.298 -1.813 -5.718 1.00 30.86 C ATOM 112 N7 DG A 6 10.089 -2.835 -5.773 1.00 29.18 N ATOM 113 C5 DG A 6 11.239 -2.433 -5.146 1.00 29.77 C ATOM 114 C6 DG A 6 12.445 -3.178 -4.923 1.00 35.80 C ATOM 115 O6 DG A 6 12.628 -4.347 -5.317 1.00 35.62 O ATOM 116 N1 DG A 6 13.392 -2.449 -4.192 1.00 26.25 N ATOM 117 C2 DG A 6 13.165 -1.134 -3.777 1.00 30.64 C ATOM 118 N2 DG A 6 14.131 -0.490 -3.085 1.00 27.33 N ATOM 119 N3 DG A 6 12.000 -0.437 -3.936 1.00 30.60 N ATOM 120 C4 DG A 6 11.105 -1.165 -4.655 1.00 33.20 C TER 121 DG A 6 HETATM 122 K K A 7 15.563 -8.246 5.774 0.50 38.85 K HETATM 123 N17 BMO A 8 12.875 -6.438 19.748 0.50 54.31 N HETATM 124 C19 BMO A 8 13.193 -5.658 18.381 1.00 55.79 C HETATM 125 C36 BMO A 8 12.814 -6.440 17.157 1.00 54.31 C HETATM 126 C22 BMO A 8 11.309 -6.462 17.115 1.00 51.45 C HETATM 127 N20 BMO A 8 10.956 -6.556 15.708 1.00 44.28 N HETATM 128 C21 BMO A 8 10.469 -7.662 15.175 1.00 40.78 C HETATM 129 C27 BMO A 8 9.129 -7.753 14.996 1.00 36.70 C HETATM 130 C26 BMO A 8 8.389 -6.668 15.428 1.00 37.02 C HETATM 131 C25 BMO A 8 7.026 -6.739 15.283 1.00 36.22 C HETATM 132 C24 BMO A 8 6.464 -7.856 14.666 1.00 38.70 C HETATM 133 C23 BMO A 8 7.206 -8.944 14.199 1.00 37.00 C HETATM 134 C28 BMO A 8 8.570 -8.893 14.397 1.00 38.08 C HETATM 135 N29 BMO A 8 9.329 -9.914 13.988 1.00 36.83 N HETATM 136 C31 BMO A 8 10.664 -9.826 14.195 1.00 36.51 C HETATM 137 C30 BMO A 8 11.257 -8.698 14.753 1.00 38.72 C HETATM 138 C34 BMO A 8 12.640 -8.613 14.943 1.00 41.26 C HETATM 139 C35 BMO A 8 13.464 -9.688 14.534 1.00 38.87 C HETATM 140 C32 BMO A 8 12.864 -10.795 13.939 1.00 37.29 C HETATM 141 C33 BMO A 8 11.470 -10.847 13.763 1.00 36.07 C HETATM 142 O HOH A 9 10.878 -8.764 20.783 1.00 33.82 O CONECT 123 124 CONECT 124 123 125 CONECT 125 124 126 CONECT 126 125 127 CONECT 127 126 128 CONECT 128 127 129 137 CONECT 129 128 130 134 CONECT 130 129 131 CONECT 131 130 132 CONECT 132 131 133 CONECT 133 132 134 CONECT 134 129 133 135 CONECT 135 134 136 CONECT 136 135 137 141 CONECT 137 128 136 138 CONECT 138 137 139 CONECT 139 138 140 CONECT 140 139 141 CONECT 141 136 140 MASTER 351 0 2 0 0 0 2 6 141 1 19 1 END