HEADER DNA 15-OCT-03 1R68 TITLE ROLE OF THE AMINO SUGAR IN DNA BINDING OF DISACCHARIDE ANTHRACYCLINES: TITLE 2 CRYSTAL STRUCTURE OF MAR70/D(CGATCG) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*TP*CP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RIGHT HANDED DNA, DOUBLE HELIX, DRUG-DNA COMPLEX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR C.TEMPERINI,M.CIRILLI,M.ASCHI,G.UGHETTO REVDAT 3 14-FEB-24 1R68 1 REMARK HETSYN REVDAT 2 24-FEB-09 1R68 1 VERSN REVDAT 1 22-FEB-05 1R68 0 JRNL AUTH C.TEMPERINI,M.CIRILLI,M.ASCHI,G.UGHETTO JRNL TITL ROLE OF THE AMINO SUGAR IN DNA BINDING OF DISACCHARIDE JRNL TITL 2 ANTHRACYCLINES: CRYSTAL STRUCTURE OF THE COMPLEX JRNL TITL 3 MAR70/D(CGATCG). JRNL REF BIOORG.MED.CHEM. V. 13 1673 2005 JRNL REFN ISSN 0968-0896 JRNL PMID 15698785 JRNL DOI 10.1016/J.BMC.2004.12.007 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.TEMPERINI,L.MESSORI,P.ORIOLI,C.DI BUGNO,F.ANIMATI, REMARK 1 AUTH 2 G.UGHETTO REMARK 1 TITL THE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN A DISACCHARIDE REMARK 1 TITL 2 ANTHRACYCLINE AND THE DNA HEXAMER D(CGATCG) REVEALS TWO REMARK 1 TITL 3 DIFFERENT BINDING SITES INVOLVING TWO DNA DUPLEXES REMARK 1 REF NUCLEIC ACIDS RES. V. 31 1464 2003 REMARK 1 REFN ISSN 0305-1048 REMARK 1 DOI 10.1093/NAR/GKG245 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.190 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.183 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 106 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 2209 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 : 47 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1R68 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020487. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : RIGAKU AFC-5R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : TEXAN, TEXSAN REMARK 200 DATA SCALING SOFTWARE : TEXSAN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6369 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 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 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, CACODYLATE, REMARK 280 SPERMINE, MPD, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K, PH 6.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 26.62500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 14.09500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 14.09500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.31250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 14.09500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 14.09500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.93750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 14.09500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 14.09500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 13.31250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 14.09500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 14.09500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.93750 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 26.62500 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 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 28.19000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 28.19000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 26.62500 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 DC A 1 C4 DC A 1 N4 -0.176 REMARK 500 DC A 1 N1 DC A 1 C2 0.208 REMARK 500 DC A 1 N1 DC A 1 C6 -0.056 REMARK 500 DC A 1 C2 DC A 1 N3 -0.141 REMARK 500 DC A 1 C4 DC A 1 C5 0.226 REMARK 500 DG A 2 C2 DG A 2 N3 0.115 REMARK 500 DG A 2 N3 DG A 2 C4 0.088 REMARK 500 DG A 2 C6 DG A 2 N1 0.102 REMARK 500 DG A 2 C5 DG A 2 N7 -0.170 REMARK 500 DG A 2 N7 DG A 2 C8 -0.058 REMARK 500 DG A 2 N9 DG A 2 C4 0.075 REMARK 500 DG A 2 C6 DG A 2 O6 0.144 REMARK 500 DA A 3 N1 DA A 3 C2 0.134 REMARK 500 DA A 3 C2 DA A 3 N3 -0.100 REMARK 500 DA A 3 N3 DA A 3 C4 -0.042 REMARK 500 DA A 3 C4 DA A 3 C5 -0.274 REMARK 500 DA A 3 C5 DA A 3 C6 0.285 REMARK 500 DA A 3 N7 DA A 3 C8 -0.048 REMARK 500 DA A 3 C8 DA A 3 N9 0.093 REMARK 500 DA A 3 N9 DA A 3 C4 -0.045 REMARK 500 DA A 3 C6 DA A 3 N6 0.077 REMARK 500 DT A 4 C1' DT A 4 N1 -0.125 REMARK 500 DT A 4 C2 DT A 4 N3 -0.114 REMARK 500 DT A 4 N3 DT A 4 C4 -0.079 REMARK 500 DT A 4 C4 DT A 4 C5 0.066 REMARK 500 DT A 4 C6 DT A 4 N1 -0.088 REMARK 500 DT A 4 C2 DT A 4 O2 0.178 REMARK 500 DT A 4 C5 DT A 4 C7 0.207 REMARK 500 DC A 5 C1' DC A 5 N1 -0.174 REMARK 500 DC A 5 C2 DC A 5 O2 0.220 REMARK 500 DC A 5 N1 DC A 5 C2 -0.062 REMARK 500 DC A 5 C2 DC A 5 N3 0.050 REMARK 500 DG A 6 N1 DG A 6 C2 -0.073 REMARK 500 DG A 6 C2 DG A 6 N3 0.180 REMARK 500 DG A 6 C4 DG A 6 C5 -0.407 REMARK 500 DG A 6 C5 DG A 6 C6 -0.123 REMARK 500 DG A 6 N7 DG A 6 C8 0.115 REMARK 500 DG A 6 N9 DG A 6 C4 0.217 REMARK 500 DG A 6 C2 DG A 6 N2 0.079 REMARK 500 DG A 6 C6 DG A 6 O6 0.161 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 N1 - C2 - N3 ANGL. DEV. = -9.1 DEGREES REMARK 500 DC A 1 C2 - N3 - C4 ANGL. DEV. = 23.6 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -19.2 DEGREES REMARK 500 DC A 1 C4 - C5 - C6 ANGL. DEV. = 6.0 DEGREES REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = 15.2 DEGREES REMARK 500 DC A 1 N3 - C4 - N4 ANGL. DEV. = 23.5 DEGREES REMARK 500 DC A 1 C5 - C4 - N4 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC A 1 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 DG A 2 O5' - P - OP1 ANGL. DEV. = 11.3 DEGREES REMARK 500 DG A 2 P - O5' - C5' ANGL. DEV. = -10.8 DEGREES REMARK 500 DG A 2 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG A 2 C6 - N1 - C2 ANGL. DEV. = -12.9 DEGREES REMARK 500 DG A 2 N1 - C2 - N3 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG A 2 C2 - N3 - C4 ANGL. DEV. = -11.2 DEGREES REMARK 500 DG A 2 N3 - C4 - C5 ANGL. DEV. = 18.8 DEGREES REMARK 500 DG A 2 C4 - C5 - C6 ANGL. DEV. = -20.7 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 19.8 DEGREES REMARK 500 DG A 2 C4 - C5 - N7 ANGL. DEV. = 7.7 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG A 2 N9 - C4 - C5 ANGL. DEV. = -7.7 DEGREES REMARK 500 DG A 2 N3 - C4 - N9 ANGL. DEV. = -11.5 DEGREES REMARK 500 DG A 2 C6 - C5 - N7 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 2 N1 - C2 - N2 ANGL. DEV. = 6.9 DEGREES REMARK 500 DG A 2 N3 - C2 - N2 ANGL. DEV. = -12.0 DEGREES REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = -21.0 DEGREES REMARK 500 DA A 3 N1 - C2 - N3 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA A 3 N3 - C4 - C5 ANGL. DEV. = 18.3 DEGREES REMARK 500 DA A 3 C4 - C5 - C6 ANGL. DEV. = -9.1 DEGREES REMARK 500 DA A 3 C5 - C6 - N1 ANGL. DEV. = -6.3 DEGREES REMARK 500 DA A 3 C4 - C5 - N7 ANGL. DEV. = 19.1 DEGREES REMARK 500 DA A 3 C5 - N7 - C8 ANGL. DEV. = -15.7 DEGREES REMARK 500 DA A 3 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 3 C8 - N9 - C4 ANGL. DEV. = -7.5 DEGREES REMARK 500 DA A 3 N9 - C4 - C5 ANGL. DEV. = -2.8 DEGREES REMARK 500 DA A 3 N3 - C4 - N9 ANGL. DEV. = -16.0 DEGREES REMARK 500 DA A 3 C6 - C5 - N7 ANGL. DEV. = -13.4 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = 7.7 DEGREES REMARK 500 DT A 4 OP1 - P - OP2 ANGL. DEV. = 14.0 DEGREES REMARK 500 DT A 4 O5' - P - OP1 ANGL. DEV. = 13.6 DEGREES REMARK 500 DT A 4 O5' - P - OP2 ANGL. DEV. = -14.7 DEGREES REMARK 500 DT A 4 P - O5' - C5' ANGL. DEV. = -13.9 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = -10.3 DEGREES REMARK 500 DT A 4 C6 - N1 - C2 ANGL. DEV. = -18.2 DEGREES REMARK 500 DT A 4 N1 - C2 - N3 ANGL. DEV. = 25.6 DEGREES REMARK 500 DT A 4 C2 - N3 - C4 ANGL. DEV. = -10.4 DEGREES REMARK 500 DT A 4 N3 - C4 - C5 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT A 4 C5 - C6 - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT A 4 N1 - C2 - O2 ANGL. DEV. = -8.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 84 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG A 2 0.09 SIDE CHAIN REMARK 500 DC A 5 0.12 SIDE CHAIN REMARK 500 DG A 6 0.08 SIDE CHAIN 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 MAR A 7 DBREF 1R68 A 1 6 PDB 1R68 1R68 1 6 SEQRES 1 A 6 DC DG DA DT DC DG HET MAR A 7 47 HETNAM MAR 4'-EPI-4'-(2-DEOXYFUCOSE)DAUNOMYCIN HETSYN MAR MAR70; DAUNOMYCIN DERIVATIVE FORMUL 2 MAR C33 H39 N O13 FORMUL 3 HOH *21(H2 O) SITE 1 AC1 11 DC A 1 DG A 2 DA A 3 DT A 4 SITE 2 AC1 11 DC A 5 DG A 6 HOH A2001 HOH A2002 SITE 3 AC1 11 HOH A2003 HOH A2009 HOH A2010 CRYST1 28.190 28.190 53.250 90.00 90.00 90.00 P 41 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 0.035474 0.000000 0.000000 0.00000 SCALE2 0.000000 0.035474 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018779 0.00000 ATOM 1 O5' DC A 1 9.387 20.318 23.217 1.00 26.88 O ATOM 2 C5' DC A 1 9.876 21.426 23.990 1.00 22.01 C ATOM 3 C4' DC A 1 11.299 21.092 24.285 1.00 19.54 C ATOM 4 O4' DC A 1 11.376 19.849 25.020 1.00 21.88 O ATOM 5 C3' DC A 1 12.128 20.898 23.020 1.00 18.00 C ATOM 6 O3' DC A 1 13.272 21.695 23.182 1.00 18.11 O ATOM 7 C2' DC A 1 12.443 19.434 22.952 1.00 16.67 C ATOM 8 C1' DC A 1 12.388 19.030 24.429 1.00 17.88 C ATOM 9 N1 DC A 1 11.968 17.694 24.679 1.00 12.06 N ATOM 10 C2 DC A 1 13.101 16.563 24.798 1.00 8.94 C ATOM 11 O2 DC A 1 14.203 17.031 24.861 1.00 14.17 O ATOM 12 N3 DC A 1 12.589 15.475 24.950 1.00 12.89 N ATOM 13 C4 DC A 1 11.423 14.838 24.978 1.00 11.43 C ATOM 14 N4 DC A 1 10.969 13.773 24.919 1.00 14.05 N ATOM 15 C5 DC A 1 10.339 16.055 24.712 1.00 15.14 C ATOM 16 C6 DC A 1 10.700 17.376 24.585 1.00 11.22 C ATOM 17 P DG A 2 13.839 22.854 22.278 1.00 25.45 P ATOM 18 OP1 DG A 2 14.802 23.583 23.131 1.00 22.64 O ATOM 19 OP2 DG A 2 12.603 23.395 21.728 1.00 23.01 O ATOM 20 O5' DG A 2 14.314 21.855 21.127 1.00 20.45 O ATOM 21 C5' DG A 2 15.679 21.502 21.319 1.00 12.98 C ATOM 22 C4' DG A 2 16.137 20.571 20.223 1.00 14.41 C ATOM 23 O4' DG A 2 15.305 19.406 20.101 1.00 16.20 O ATOM 24 C3' DG A 2 16.084 21.211 18.837 1.00 16.05 C ATOM 25 O3' DG A 2 17.236 20.796 18.112 1.00 25.21 O ATOM 26 C2' DG A 2 14.792 20.731 18.226 1.00 17.13 C ATOM 27 C1' DG A 2 14.877 19.265 18.743 1.00 20.98 C ATOM 28 N9 DG A 2 13.651 18.387 18.748 1.00 18.76 N ATOM 29 C8 DG A 2 12.310 18.733 18.759 1.00 12.49 C ATOM 30 N7 DG A 2 11.499 17.791 18.662 1.00 17.95 N ATOM 31 C5 DG A 2 12.221 16.883 18.290 1.00 18.47 C ATOM 32 C6 DG A 2 12.096 15.489 18.252 1.00 10.19 C ATOM 33 O6 DG A 2 10.961 14.704 18.204 1.00 13.31 O ATOM 34 N1 DG A 2 13.122 14.406 18.316 1.00 15.54 N ATOM 35 C2 DG A 2 14.394 14.904 18.434 1.00 13.30 C ATOM 36 N2 DG A 2 15.511 14.127 18.331 1.00 12.33 N ATOM 37 N3 DG A 2 14.818 16.259 18.659 1.00 13.71 N ATOM 38 C4 DG A 2 13.559 16.950 18.580 1.00 14.22 C ATOM 39 P DA A 3 17.999 21.865 17.214 1.00 25.16 P ATOM 40 OP1 DA A 3 18.609 22.640 18.289 1.00 28.22 O ATOM 41 OP2 DA A 3 17.086 22.321 16.171 1.00 32.91 O ATOM 42 O5' DA A 3 19.144 20.921 16.696 1.00 19.94 O ATOM 43 C5' DA A 3 20.077 20.286 17.581 1.00 21.80 C ATOM 44 C4' DA A 3 20.377 18.942 16.964 1.00 13.78 C ATOM 45 O4' DA A 3 19.204 18.091 17.008 1.00 18.42 O ATOM 46 C3' DA A 3 20.788 19.030 15.504 1.00 12.73 C ATOM 47 O3' DA A 3 21.965 18.252 15.393 1.00 16.31 O ATOM 48 C2' DA A 3 19.632 18.489 14.732 1.00 14.69 C ATOM 49 C1' DA A 3 18.969 17.517 15.731 1.00 17.92 C ATOM 50 N9 DA A 3 17.484 17.283 15.685 1.00 12.91 N ATOM 51 C8 DA A 3 16.496 18.365 15.655 1.00 11.24 C ATOM 52 N7 DA A 3 15.318 18.068 15.311 1.00 12.68 N ATOM 53 C5 DA A 3 15.668 16.746 15.414 1.00 11.69 C ATOM 54 C6 DA A 3 14.530 15.566 15.000 1.00 11.68 C ATOM 55 N6 DA A 3 13.149 15.854 14.940 1.00 14.23 N ATOM 56 N1 DA A 3 15.106 14.317 14.921 1.00 11.24 N ATOM 57 C2 DA A 3 16.533 14.201 15.268 1.00 14.45 C ATOM 58 N3 DA A 3 17.320 15.146 15.324 1.00 13.38 N ATOM 59 C4 DA A 3 16.671 16.273 15.395 1.00 12.34 C ATOM 60 P DT A 4 22.788 18.120 14.025 1.00 22.89 P ATOM 61 OP1 DT A 4 24.164 17.967 14.511 1.00 22.46 O ATOM 62 OP2 DT A 4 22.095 19.163 13.274 1.00 23.35 O ATOM 63 O5' DT A 4 21.972 16.979 13.246 1.00 17.37 O ATOM 64 C5' DT A 4 22.370 15.737 13.798 1.00 13.01 C ATOM 65 C4' DT A 4 21.787 14.577 12.985 1.00 15.13 C ATOM 66 O4' DT A 4 20.366 14.649 13.029 1.00 14.78 O ATOM 67 C3' DT A 4 22.165 14.554 11.501 1.00 12.89 C ATOM 68 O3' DT A 4 22.810 13.324 11.202 1.00 16.44 O ATOM 69 C2' DT A 4 20.887 14.688 10.721 1.00 15.33 C ATOM 70 C1' DT A 4 19.856 14.241 11.746 1.00 15.28 C ATOM 71 N1 DT A 4 18.717 14.953 11.770 1.00 13.33 N ATOM 72 C2 DT A 4 17.494 14.397 11.750 1.00 12.68 C ATOM 73 O2 DT A 4 17.497 13.000 11.790 1.00 14.82 O ATOM 74 N3 DT A 4 16.280 14.729 11.784 1.00 13.21 N ATOM 75 C4 DT A 4 16.021 16.004 11.848 1.00 10.07 C ATOM 76 O4 DT A 4 14.989 16.609 11.878 1.00 13.54 O ATOM 77 C5 DT A 4 17.289 16.825 11.810 1.00 12.25 C ATOM 78 C7 DT A 4 17.076 18.512 11.898 1.00 12.90 C ATOM 79 C6 DT A 4 18.463 16.216 11.843 1.00 12.14 C ATOM 80 P DC A 5 23.748 13.060 9.918 1.00 22.45 P ATOM 81 OP1 DC A 5 24.471 11.833 10.288 1.00 28.40 O ATOM 82 OP2 DC A 5 24.143 14.364 9.446 1.00 18.36 O ATOM 83 O5' DC A 5 22.599 12.737 8.830 1.00 19.07 O ATOM 84 C5' DC A 5 22.004 11.433 8.885 1.00 12.89 C ATOM 85 C4' DC A 5 20.861 11.487 7.899 1.00 13.34 C ATOM 86 O4' DC A 5 19.857 12.415 8.376 1.00 14.16 O ATOM 87 C3' DC A 5 21.204 11.987 6.508 1.00 13.58 C ATOM 88 O3' DC A 5 20.555 11.187 5.523 1.00 18.36 O ATOM 89 C2' DC A 5 20.674 13.378 6.440 1.00 15.27 C ATOM 90 C1' DC A 5 19.359 13.131 7.225 1.00 15.94 C ATOM 91 N1 DC A 5 18.835 14.175 7.781 1.00 13.74 N ATOM 92 C2 DC A 5 17.570 14.490 8.067 1.00 14.20 C ATOM 93 O2 DC A 5 16.979 13.173 8.288 1.00 13.09 O ATOM 94 N3 DC A 5 16.471 15.321 8.334 1.00 15.26 N ATOM 95 C4 DC A 5 17.088 16.545 8.203 1.00 21.53 C ATOM 96 N4 DC A 5 16.400 17.639 8.555 1.00 12.67 N ATOM 97 C5 DC A 5 18.534 16.691 8.052 1.00 12.19 C ATOM 98 C6 DC A 5 19.178 15.513 7.718 1.00 12.45 C ATOM 99 P DG A 6 21.315 10.081 4.650 1.00 25.60 P ATOM 100 OP1 DG A 6 21.819 9.046 5.570 1.00 25.87 O ATOM 101 OP2 DG A 6 22.117 10.992 3.816 1.00 19.29 O ATOM 102 O5' DG A 6 20.073 9.534 3.849 1.00 21.78 O ATOM 103 C5' DG A 6 19.328 8.525 4.531 1.00 13.35 C ATOM 104 C4' DG A 6 18.345 7.940 3.533 1.00 17.30 C ATOM 105 O4' DG A 6 17.368 8.939 3.148 1.00 16.34 O ATOM 106 C3' DG A 6 18.949 7.467 2.222 1.00 11.02 C ATOM 107 O3' DG A 6 18.135 6.387 1.785 1.00 18.07 O ATOM 108 C2' DG A 6 18.917 8.682 1.351 1.00 16.21 C ATOM 109 C1' DG A 6 17.581 9.299 1.785 1.00 18.23 C ATOM 110 N9 DG A 6 17.561 10.761 1.680 1.00 14.24 N ATOM 111 C8 DG A 6 18.657 11.532 1.649 1.00 15.24 C ATOM 112 N7 DG A 6 18.378 12.923 1.597 1.00 18.95 N ATOM 113 C5 DG A 6 17.008 12.647 1.635 1.00 13.93 C ATOM 114 C6 DG A 6 16.185 13.646 1.574 1.00 11.59 C ATOM 115 O6 DG A 6 16.369 15.031 1.619 1.00 15.06 O ATOM 116 N1 DG A 6 14.795 13.625 1.489 1.00 11.57 N ATOM 117 C2 DG A 6 14.457 12.373 1.393 1.00 12.92 C ATOM 118 N2 DG A 6 13.132 11.888 1.551 1.00 12.10 N ATOM 119 N3 DG A 6 15.349 11.174 1.553 1.00 11.55 N ATOM 120 C4 DG A 6 16.459 11.878 1.409 1.00 12.38 C TER 121 DG A 6 HETATM 122 C1 MAR A 7 15.493 18.545 5.079 1.00 21.42 C HETATM 123 C2 MAR A 7 16.691 19.265 5.065 1.00 21.39 C HETATM 124 C3 MAR A 7 17.918 18.590 4.977 1.00 19.98 C HETATM 125 C4 MAR A 7 17.938 17.207 4.799 1.00 13.36 C HETATM 126 O4 MAR A 7 19.213 16.599 4.786 1.00 19.58 O HETATM 127 C5 MAR A 7 16.744 16.475 4.920 1.00 13.89 C HETATM 128 C6 MAR A 7 16.732 15.080 4.822 1.00 12.55 C HETATM 129 O6 MAR A 7 17.889 14.396 4.580 1.00 16.98 O HETATM 130 C7 MAR A 7 15.537 14.361 4.890 1.00 12.45 C HETATM 131 C8 MAR A 7 15.500 12.969 4.755 1.00 13.70 C HETATM 132 O8 MAR A 7 16.651 12.234 4.756 1.00 15.52 O HETATM 133 C9 MAR A 7 14.287 12.255 4.870 1.00 12.23 C HETATM 134 C10 MAR A 7 14.411 10.778 5.026 1.00 15.46 C HETATM 135 O10 MAR A 7 15.009 10.466 6.331 1.00 15.13 O HETATM 136 C11 MAR A 7 13.106 9.981 4.843 1.00 14.66 C HETATM 137 C12 MAR A 7 11.936 10.759 5.508 1.00 15.45 C HETATM 138 O12 MAR A 7 12.122 10.951 6.929 1.00 16.41 O HETATM 139 C13 MAR A 7 10.679 9.943 5.253 1.00 21.19 C HETATM 140 O13 MAR A 7 9.995 10.342 4.120 1.00 18.83 O HETATM 141 C14 MAR A 7 10.328 8.825 6.157 1.00 15.22 C HETATM 142 C15 MAR A 7 11.823 12.163 4.854 1.00 13.47 C HETATM 143 C16 MAR A 7 13.083 12.940 4.915 1.00 8.67 C HETATM 144 C17 MAR A 7 13.117 14.346 4.902 1.00 12.73 C HETATM 145 O17 MAR A 7 11.904 15.061 4.906 1.00 16.41 O HETATM 146 C18 MAR A 7 14.330 15.039 4.949 1.00 10.59 C HETATM 147 C19 MAR A 7 14.334 16.443 5.004 1.00 17.17 C HETATM 148 O19 MAR A 7 13.184 17.080 4.820 1.00 19.94 O HETATM 149 C20 MAR A 7 15.544 17.144 4.957 1.00 14.11 C HETATM 150 C21 MAR A 7 20.560 17.228 4.769 1.00 23.64 C HETATM 151 C1' MAR A 7 15.838 9.339 6.542 1.00 15.43 C HETATM 152 C2' MAR A 7 17.068 9.648 7.461 1.00 18.00 C HETATM 153 C3' MAR A 7 16.518 10.078 8.838 1.00 21.37 C HETATM 154 N3' MAR A 7 17.648 10.467 9.814 1.00 18.97 N HETATM 155 C4' MAR A 7 15.629 8.969 9.413 1.00 12.39 C HETATM 156 O4' MAR A 7 16.516 7.835 9.574 1.00 25.00 O HETATM 157 C5' MAR A 7 14.505 8.577 8.419 1.00 18.00 C HETATM 158 O5' MAR A 7 15.085 8.209 7.135 1.00 18.48 O HETATM 159 C6' MAR A 7 13.621 7.405 8.900 1.00 26.57 C HETATM 160 CB1 MAR A 7 16.359 6.968 10.670 1.00 46.94 C HETATM 161 CB2 MAR A 7 16.622 5.476 10.384 1.00 58.59 C HETATM 162 CB3 MAR A 7 18.154 5.296 10.373 1.00 62.75 C HETATM 163 OB3 MAR A 7 18.493 3.896 9.998 1.00 53.65 O HETATM 164 CB4 MAR A 7 18.782 5.709 11.714 1.00 58.37 C HETATM 165 OB4 MAR A 7 20.240 5.652 11.636 1.00 81.98 O HETATM 166 CB5 MAR A 7 18.257 7.052 12.251 1.00 50.13 C HETATM 167 OB5 MAR A 7 16.916 7.354 11.941 1.00 43.19 O HETATM 168 CB6 MAR A 7 18.459 7.206 13.789 1.00 52.56 C HETATM 169 O HOH A2001 16.700 9.920 12.524 1.00 34.10 O HETATM 170 O HOH A2002 19.810 8.641 9.823 1.00 29.56 O HETATM 171 O HOH A2003 19.945 14.730 2.651 1.00 23.35 O HETATM 172 O HOH A2004 7.326 12.986 24.739 1.00 49.31 O HETATM 173 O HOH A2005 13.028 18.800 11.063 1.00 52.03 O HETATM 174 O HOH A2006 17.495 20.138 8.552 1.00 33.83 O HETATM 175 O HOH A2007 13.134 19.695 15.283 1.00 39.04 O HETATM 176 O HOH A2008 22.750 15.838 7.712 1.00 28.18 O HETATM 177 O HOH A2009 15.915 6.134 6.160 1.00 47.80 O HETATM 178 O HOH A2010 16.077 18.992 24.805 1.00 32.23 O HETATM 179 O HOH A2011 16.476 18.594 27.752 1.00 42.12 O HETATM 180 O HOH A2012 17.827 16.720 1.129 1.00 41.69 O HETATM 181 O HOH A2013 14.076 8.332 1.841 1.00 36.48 O HETATM 182 O HOH A2014 20.752 18.794 10.876 1.00 38.79 O HETATM 183 O HOH A2015 20.132 6.624 7.696 1.00 59.78 O HETATM 184 O HOH A2016 25.385 10.641 6.159 1.00 47.56 O HETATM 185 O HOH A2017 22.382 11.114 0.849 1.00 78.88 O HETATM 186 O HOH A2018 10.891 18.367 14.863 1.00 89.61 O HETATM 187 O HOH A2019 15.369 5.572 1.540 1.00 92.19 O HETATM 188 O HOH A2020 24.202 8.129 7.163 1.00 59.22 O HETATM 189 O HOH A2021 8.689 11.154 24.875 1.00 65.50 O CONECT 122 123 149 CONECT 123 122 124 CONECT 124 123 125 CONECT 125 124 126 127 CONECT 126 125 150 CONECT 127 125 128 149 CONECT 128 127 129 130 CONECT 129 128 CONECT 130 128 131 146 CONECT 131 130 132 133 CONECT 132 131 CONECT 133 131 134 143 CONECT 134 133 135 136 CONECT 135 134 151 CONECT 136 134 137 CONECT 137 136 138 139 142 CONECT 138 137 CONECT 139 137 140 141 CONECT 140 139 CONECT 141 139 CONECT 142 137 143 CONECT 143 133 142 144 CONECT 144 143 145 146 CONECT 145 144 CONECT 146 130 144 147 CONECT 147 146 148 149 CONECT 148 147 CONECT 149 122 127 147 CONECT 150 126 CONECT 151 135 152 158 CONECT 152 151 153 CONECT 153 152 154 155 CONECT 154 153 CONECT 155 153 156 157 CONECT 156 155 160 CONECT 157 155 158 159 CONECT 158 151 157 CONECT 159 157 CONECT 160 156 161 167 CONECT 161 160 162 CONECT 162 161 163 164 CONECT 163 162 CONECT 164 162 165 166 CONECT 165 164 CONECT 166 164 167 168 CONECT 167 160 166 CONECT 168 166 MASTER 356 0 1 0 0 0 3 6 188 1 47 1 END