HEADER DNA 23-JUN-15 2N4M TITLE BASE-DISPLACED INTERCALATED STRUCTURE OF THE N-(2'DEOXYGUANOSIN-8-YL)- TITLE 2 3-AMINOBENZANTHRONE DNA ADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.A.POLITICA,M.P.STONE,C.K.MALIK,A.K.BASU REVDAT 2 01-MAY-24 2N4M 1 REMARK LINK REVDAT 1 06-JUL-16 2N4M 0 JRNL AUTH D.A.POLITICA,C.K.MALIK,A.K.BASU,M.P.STONE JRNL TITL BASE-DISPLACED INTERCALATED STRUCTURE OF THE JRNL TITL 2 N-(2'-DEOXYGUANOSIN-8-YL)-3-AMINOBENZANTHRONE DNA ADDUCT. JRNL REF CHEM.RES.TOXICOL. V. 28 2253 2015 JRNL REFN ISSN 0893-228X JRNL PMID 26641105 JRNL DOI 10.1021/ACS.CHEMRESTOX.5B00277 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000104415. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 288 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 110; 110 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 352 UM DNA (5' REMARK 210 -D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3'), 352 UM DNA (5'- REMARK 210 D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), 10 MM SODIUM REMARK 210 PHOSPHATE, 100 MM SODIUM CHLORIDE, 50 UM EDTA, 100% D2O; 521 UM REMARK 210 DNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3'), 521 UM REMARK 210 DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), 10 MM SODIUM REMARK 210 PHOSPHATE, 100 MM SODIUM CHLORIDE, 50 UM EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, TOPSPIN, MARDIGRAS, REMARK 210 CORMA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 85 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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, 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: 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 8 DC B 20 C5' DC B 20 C4' 0.044 REMARK 500 8 DC B 20 C4 DC B 20 C5 0.052 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 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA B 13 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 13 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 13 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA B 16 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 16 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA B 16 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA B 17 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC B 18 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA B 19 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA B 19 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC B 20 N3 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 21 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC B 22 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA B 23 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA B 23 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 23 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DC B 24 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG A 11 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DA B 13 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA B 13 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA B 13 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DA B 16 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA B 16 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DA B 16 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA B 17 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 336 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 1 DG A 1 0.05 SIDE CHAIN REMARK 500 1 DA B 19 0.08 SIDE CHAIN REMARK 500 1 DG B 21 0.07 SIDE CHAIN REMARK 500 2 DG A 1 0.06 SIDE CHAIN REMARK 500 2 DA B 19 0.06 SIDE CHAIN REMARK 500 2 DG B 21 0.07 SIDE CHAIN REMARK 500 3 DG A 1 0.05 SIDE CHAIN REMARK 500 3 DT A 2 0.07 SIDE CHAIN REMARK 500 3 DA B 19 0.08 SIDE CHAIN REMARK 500 3 DG B 21 0.07 SIDE CHAIN REMARK 500 4 DG A 1 0.06 SIDE CHAIN REMARK 500 4 DA B 19 0.06 SIDE CHAIN REMARK 500 5 DG A 1 0.06 SIDE CHAIN REMARK 500 5 DA B 19 0.07 SIDE CHAIN REMARK 500 5 DG B 21 0.06 SIDE CHAIN REMARK 500 6 DG A 1 0.06 SIDE CHAIN REMARK 500 6 DA B 19 0.07 SIDE CHAIN REMARK 500 6 DG B 21 0.07 SIDE CHAIN REMARK 500 7 DG A 1 0.05 SIDE CHAIN REMARK 500 7 DA B 19 0.08 SIDE CHAIN REMARK 500 7 DG B 21 0.07 SIDE CHAIN REMARK 500 8 DA B 19 0.07 SIDE CHAIN REMARK 500 8 DC B 20 0.11 SIDE CHAIN REMARK 500 8 DG B 21 0.07 SIDE CHAIN REMARK 500 9 DG A 1 0.06 SIDE CHAIN REMARK 500 9 DA B 19 0.09 SIDE CHAIN REMARK 500 9 DG B 21 0.06 SIDE CHAIN REMARK 500 10 DG A 1 0.06 SIDE CHAIN REMARK 500 10 DT A 2 0.07 SIDE CHAIN REMARK 500 10 DA B 19 0.08 SIDE CHAIN REMARK 500 10 DG B 21 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25672 RELATED DB: BMRB DBREF 2N4M A 1 12 PDB 2N4M 2N4M 1 12 DBREF 2N4M B 13 24 PDB 2N4M 2N4M 13 24 SEQRES 1 A 12 DG DT DG DC 4E9 DT DG DT DT DT DG DT SEQRES 1 B 12 DA DC DA DA DA DC DA DC DG DC DA DC HET 4E9 A 5 61 HETNAM 4E9 2'-DEOXY-8-[(7-OXO-7H-BENZO[DE]ANTHRACEN-3-YL) HETNAM 2 4E9 AMINO]GUANOSINE 5'-(DIHYDROGEN PHOSPHATE) FORMUL 1 4E9 C27 H23 N6 O8 P LINK O3' DC A 4 P 4E9 A 5 1555 1555 1.61 LINK O3' 4E9 A 5 P DT A 6 1555 1555 1.62 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1