HEADER DNA 20-APR-08 2ROU TITLE STEREOSPECIFIC CONFORMATIONS OF N2-DG 1R-TRANS-ANTI- TITLE 2 BENZO[C]PHENANTHRENE DNA ADDUCTS: 3'-INTERCALATION OF THE 1R ADDUCT TITLE 3 AND 5'-MINOR GROOVE ORIENTATION OF THE 1S ADDUCT IN AN ITERATED (CG)3 TITLE 4 REPEAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*DAP*DTP*DCP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DAP*DTP*DG)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*DCP*DAP*DTP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DGP*DAP*DT)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS N2-DG 1R-TRANS-ANTI-BENZO[C]PHENANTHRENE, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR Y.WANG,H.KROTH,H.YAGI,J.M.SAYER,S.KUMAR,D.M.JERINA,M.P.STONE REVDAT 3 29-MAY-24 2ROU 1 REMARK REVDAT 2 16-MAR-22 2ROU 1 REMARK LINK REVDAT 1 03-MAR-09 2ROU 0 JRNL AUTH Y.WANG,N.C.SCHNETZ-BOUTAUD,H.KROTH,H.YAGI,J.M.SAYER,S.KUMAR, JRNL AUTH 2 D.M.JERINA,M.P.STONE JRNL TITL 3'-INTERCALATION OF A N2-DG JRNL TITL 2 1R-TRANS-ANTI-BENZO[C]PHENANTHRENE DNA ADDUCT IN AN ITERATED JRNL TITL 3 (CG)3 REPEAT JRNL REF CHEM.RES.TOXICOL. V. 21 1348 2008 JRNL REFN ISSN 0893-228X JRNL PMID 18549249 JRNL DOI 10.1021/TX7004103 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER II REMARK 3 AUTHORS : REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH, REMARK 3 WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ROU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000150107. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 5 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10MM [U-100% 2H] DNA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AM REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA A 1 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 6 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG A 6 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 11 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 11 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 11 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DT A 12 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 13 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 13 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 15 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT B 16 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG B 17 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG B 17 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 19 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG B 20 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 20 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DC B 23 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 24 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG B 24 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG B 24 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA B 25 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 25 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 52 ANGLE DEVIATIONS. 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 BPJ A 27 DBREF 2ROU A 1 13 PDB 2ROU 2ROU 1 13 DBREF 2ROU B 14 26 PDB 2ROU 2ROU 14 26 SEQRES 1 A 13 DA DT DC DG DC DG DC DG DG DC DA DT DG SEQRES 1 B 13 DC DA DT DG DC DC DG DC DG DC DG DA DT HET BPJ A 27 36 HETNAM BPJ (1R)-1,2,3,4-TETRAHYDRO-BENZO[C]PHENANTHRENE-2,3,4- HETNAM 2 BPJ TRIOL HETSYN BPJ 1R-TRANS-ANTI-BENZO[C]PHENANTHRENE FORMUL 3 BPJ C18 H16 O3 LINK N2 DG A 6 C1 BPJ A 27 1555 1555 1.47 SITE 1 AC1 6 DC A 5 DG A 6 DC A 7 DG B 20 SITE 2 AC1 6 DC B 21 DG B 22 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