HEADER DNA/ANTIBIOTIC 19-SEP-11 3TVB TITLE A HIGHLY SYMMETRIC DNA G-4 QUADRUPLEX/DRUG COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*GP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC OLIGOMER KEYWDS G-4 QUADRUPLEX, DAUNOMYCIN, DNA-DRUG COMPLEX, DNA-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.R.CLARK,P.D.PYTEL,C.J.SQUIRE REVDAT 4 28-FEB-24 3TVB 1 REMARK LINK REVDAT 3 29-JAN-20 3TVB 1 REMARK REVDAT 2 11-JUL-12 3TVB 1 JRNL REVDAT 1 14-MAR-12 3TVB 0 JRNL AUTH G.R.CLARK,P.D.PYTEL,C.J.SQUIRE JRNL TITL THE HIGH-RESOLUTION CRYSTAL STRUCTURE OF A PARALLEL JRNL TITL 2 INTERMOLECULAR DNA G-4 QUADRUPLEX/DRUG COMPLEX EMPLOYING SYN JRNL TITL 3 GLYCOSYL LINKAGES. JRNL REF NUCLEIC ACIDS RES. V. 40 5731 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22373921 JRNL DOI 10.1093/NAR/GKS193 REMARK 2 REMARK 2 RESOLUTION. 1.08 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) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R 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) : 0.164 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.162 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 11.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1677 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 15269 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.161 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.159 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 11.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1598 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 14501 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 170 REMARK 3 HETEROGEN ATOMS : 162 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 430.19 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2579 REMARK 3 NUMBER OF RESTRAINTS : 2250 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.000 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.072 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.019 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3TVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000067964. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-04 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 : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.006 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21428 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.080 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 66.90 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 81.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 15.14 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NATRIX NR46 DROPLETS 0.005 M MAGNESIUM REMARK 280 SULFATE, 0.05 M TRIS HCL BUFFER AT PH 8.5, 35% W/V 1,6-HEXANE REMARK 280 DIOL, SITTING DROP, TEMPERATURE 277K, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 20.10450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.10450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.91550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.10450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.10450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.91550 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 20.10450 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 20.10450 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 24.91550 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 20.10450 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 20.10450 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 24.91550 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -265.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 40.20900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 40.20900 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 40.20900 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 40.20900 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 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 NA NA A 13 LIES ON A SPECIAL POSITION. REMARK 375 NA NA A 14 LIES ON A SPECIAL POSITION. REMARK 375 NA NA A 15 LIES ON A SPECIAL POSITION. REMARK 375 NA NA B 16 LIES ON A SPECIAL POSITION. REMARK 375 NA NA B 17 LIES ON A SPECIAL POSITION. REMARK 375 NA NA B 18 LIES ON A SPECIAL POSITION. REMARK 375 NA NA B 19 LIES ON A SPECIAL POSITION. REMARK 375 NA NA B 20 LIES ON A SPECIAL POSITION. REMARK 375 MG MG B 21 LIES ON A SPECIAL POSITION. REMARK 375 MG MG B 22 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 103 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 106 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 B 199 O HOH B 203 2.17 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 1 N1 DG A 1 C2 0.049 REMARK 500 DG A 1 C4 DG A 1 C5 0.055 REMARK 500 DG A 1 C5 DG A 1 C6 -0.076 REMARK 500 DG A 1 C5 DG A 1 N7 -0.041 REMARK 500 DG A 1 N7 DG A 1 C8 0.090 REMARK 500 DG A 1 N9 DG A 1 C4 -0.058 REMARK 500 DG A 2 C5' DG A 2 C4' 0.062 REMARK 500 DG A 2 N1 DG A 2 C2 0.049 REMARK 500 DG A 2 C6 DG A 2 N1 -0.045 REMARK 500 DG A 2 C8 DG A 2 N9 -0.055 REMARK 500 DG A 3 P DG A 3 OP2 -0.118 REMARK 500 DG A 3 P DG A 3 O5' -0.077 REMARK 500 DG A 3 C5' DG A 3 C4' -0.067 REMARK 500 DG A 3 O3' DG A 3 C3' 0.159 REMARK 500 DG A 3 N1 DG A 3 C2 0.052 REMARK 500 DG A 3 C5 DG A 3 C6 0.072 REMARK 500 DG A 3 C8 DG A 3 N9 0.046 REMARK 500 DG A 4 P DG A 4 OP1 0.103 REMARK 500 DG A 4 C4' DG A 4 C3' -0.075 REMARK 500 DG A 4 O4' DG A 4 C4' 0.066 REMARK 500 DG A 4 N1 DG A 4 C2 0.063 REMARK 500 DG A 4 C6 DG A 4 N1 -0.098 REMARK 500 DG A 4 C8 DG A 4 N9 0.092 REMARK 500 DG A 4 C2 DG A 4 N2 -0.070 REMARK 500 DG B 5 C5' DG B 5 C4' -0.067 REMARK 500 DG B 6 C3' DG B 6 C2' -0.061 REMARK 500 DG B 7 C2 DG B 7 N3 0.079 REMARK 500 DG B 7 C5 DG B 7 N7 -0.042 REMARK 500 DG B 7 N7 DG B 7 C8 0.047 REMARK 500 DG B 8 C5' DG B 8 C4' -0.143 REMARK 500 DG B 8 C3' DG B 8 C2' 0.078 REMARK 500 DG B 8 N3 DG B 8 C4 -0.059 REMARK 500 DG B 8 C4 DG B 8 C5 0.047 REMARK 500 DG B 8 C2 DG B 8 N2 -0.109 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 1 N1 - C2 - N3 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG A 1 C2 - N3 - C4 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 1 N3 - C4 - C5 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 1 C8 - N9 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG A 2 C4 - C5 - N7 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 2 N9 - C4 - C5 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG A 3 C2 - N3 - C4 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 4 O5' - C5' - C4' ANGL. DEV. = -8.9 DEGREES REMARK 500 DG A 4 P - O5' - C5' ANGL. DEV. = -10.2 DEGREES REMARK 500 DG A 4 C4' - C3' - C2' ANGL. DEV. = 7.2 DEGREES REMARK 500 DG A 4 C3' - C2' - C1' ANGL. DEV. = -7.1 DEGREES REMARK 500 DG A 4 N1 - C2 - N3 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG A 4 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A 4 N3 - C2 - N2 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG B 5 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DG B 5 N1 - C2 - N3 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG B 5 C2 - N3 - C4 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 5 N3 - C2 - N2 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 6 C4 - C5 - N7 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG B 7 O5' - C5' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 DG B 8 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG B 8 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG B 8 N1 - C2 - N3 ANGL. DEV. = -6.8 DEGREES REMARK 500 DG B 8 C2 - N3 - C4 ANGL. DEV. = 6.5 DEGREES REMARK 500 DG B 8 C5 - N7 - C8 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 8 C8 - N9 - C4 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 8 N9 - C4 - C5 ANGL. DEV. = -2.8 DEGREES REMARK 500 DG B 8 N3 - C4 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 111 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH B 178 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH B 196 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH B 206 DISTANCE = 7.29 ANGSTROMS 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 NA A 13 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 2 O6 72.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 14 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 2 O6 REMARK 620 2 DG A 3 O6 75.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 15 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DG A 4 O6 68.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 16 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 5 O6 REMARK 620 2 DG B 6 O6 72.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 17 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 6 O6 REMARK 620 2 DG B 7 O6 75.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 18 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 7 O6 REMARK 620 2 DG B 8 O6 68.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 19 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 109 O REMARK 620 2 HOH B 110 O 44.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 22 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 102 O REMARK 620 2 HOH B 106 O 91.7 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DM1 A 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DM1 A 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 15 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DM1 B 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DM1 B 12 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 16 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 17 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 18 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 19 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 21 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 22 DBREF 3TVB A 1 4 PDB 3TVB 3TVB 1 4 DBREF 3TVB B 5 8 PDB 3TVB 3TVB 5 8 SEQRES 1 A 4 DG DG DG DG SEQRES 1 B 4 DG DG DG DG HET DM1 A 9 38 HET DM1 A 10 38 HET NA A 13 1 HET NA A 14 1 HET NA A 15 1 HET DM1 B 11 38 HET DM1 B 12 38 HET NA B 16 1 HET NA B 17 1 HET NA B 18 1 HET NA B 19 1 HET NA B 20 1 HET MG B 21 1 HET MG B 22 1 HETNAM DM1 DAUNOMYCIN HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETSYN DM1 DAUNORUBICIN FORMUL 3 DM1 4(C27 H29 N O10) FORMUL 5 NA 8(NA 1+) FORMUL 15 MG 2(MG 2+) FORMUL 17 HOH *110(H2 O) LINK O6 DG A 1 NA NA A 13 1555 1555 2.77 LINK O6 DG A 2 NA NA A 13 1555 1555 2.86 LINK O6 DG A 2 NA NA A 14 1555 1555 2.80 LINK O6 DG A 3 NA NA A 14 1555 1555 2.63 LINK O6 DG A 3 NA NA A 15 1555 1555 3.20 LINK O6 DG A 4 NA NA A 15 1555 1555 2.38 LINK O6 DG B 5 NA NA B 16 1555 1555 2.78 LINK O6 DG B 6 NA NA B 16 1555 1555 2.88 LINK O6 DG B 6 NA NA B 17 1555 1555 2.78 LINK O6 DG B 7 NA NA B 17 1555 1555 2.65 LINK O6 DG B 7 NA NA B 18 1555 1555 3.12 LINK O6 DG B 8 NA NA B 18 1555 1555 2.46 LINK NA NA B 19 O HOH B 109 1555 1555 2.44 LINK NA NA B 19 O HOH B 110 1555 1555 2.44 LINK MG MG B 21 O HOH B 111 1555 1555 1.98 LINK MG MG B 22 O HOH B 102 1555 1555 2.15 LINK MG MG B 22 O HOH B 106 1555 1555 2.38 SITE 1 AC1 6 DG A 1 DG A 2 DM1 A 10 HOH A 123 SITE 2 AC1 6 HOH A 149 HOH A 201 SITE 1 AC2 10 DM1 A 9 HOH A 123 HOH A 127 HOH A 128 SITE 2 AC2 10 HOH A 151 HOH A 179 HOH A 187 HOH A 200 SITE 3 AC2 10 HOH A 201 DM1 B 11 SITE 1 AC3 3 DG A 1 DG A 2 NA A 14 SITE 1 AC4 4 DG A 2 DG A 3 NA A 13 NA A 15 SITE 1 AC5 3 DG A 3 DG A 4 NA A 14 SITE 1 AC6 8 DM1 A 10 DM1 B 12 HOH B 113 HOH B 125 SITE 2 AC6 8 HOH B 126 HOH B 132 HOH B 140 HOH B 170 SITE 1 AC7 10 DG B 5 DG B 6 DM1 B 11 HOH B 102 SITE 2 AC7 10 HOH B 113 HOH B 145 HOH B 150 HOH B 159 SITE 3 AC7 10 HOH B 162 HOH B 198 SITE 1 AC8 4 DG B 5 DG B 6 NA B 17 MG B 22 SITE 1 AC9 4 DG B 6 DG B 7 NA B 16 NA B 18 SITE 1 BC1 3 DG B 7 DG B 8 NA B 17 SITE 1 BC2 2 HOH B 109 HOH B 110 SITE 1 BC4 1 HOH B 111 SITE 1 BC5 4 DG B 5 NA B 16 HOH B 102 HOH B 106 CRYST1 40.209 40.209 49.831 90.00 90.00 90.00 I 4 16 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 0.024870 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020068 0.00000