HEADER DNA 20-NOV-02 1N8C TITLE SOLUTION STRUCTURE OF A CIS-OPENED (10R)-N6-DEOXYADENOSINE TITLE 2 ADDUCT OF (9S,10R)-(9,10)-EPOXY-7,8,9,10- TITLE 3 TETRAHYDROBENZO[A]PYRENE IN A DNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*TP*CP*AP*CP*GP*AP*GP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*CP*TP*CP*GP*TP*GP*AP*CP*CP*G)-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 BENZO[A]PYRENE, 7,8,9,10-TETRAHYDROBENZO[A]PYRENE, DNA EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR D.E.VOLK,V.THIVIYANATHAN,J.S.RICE,B.A.LUXON,J.H.SHAH,H.YAGI, AUTHOR 2 J.M.SAYER,H.J.C.YEH,D.M.JERINA,D.G.GORENSTEIN REVDAT 2 24-FEB-09 1N8C 1 VERSN REVDAT 1 14-FEB-03 1N8C 0 JRNL AUTH D.E.VOLK,V.THIVIYANATHAN,J.S.RICE,B.A.LUXON, JRNL AUTH 2 J.H.SHAH,H.YAGI,J.M.SAYER,H.J.C.YEH,D.M.JERINA, JRNL AUTH 3 D.G.GORENSTEIN JRNL TITL SOLUTION STRUCTURE OF A CIS-OPENED JRNL TITL 2 (10R)-N6-DEOXYADENOSINE ADDUCT OF JRNL TITL 3 (9S,10R)-(9,10)-EPOXY-7,8,9,10- JRNL TITL 4 TETRAHYDROBENZO[A]PYRENE IN A DNA DUPLEX JRNL REF BIOCHEMISTRY V. 42 1410 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12578353 JRNL DOI 10.1021/BI026745U REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.0, 6.0, AND 7.0 REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1N8C COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-02. REMARK 100 THE RCSB ID CODE IS RCSB017645. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 288 REMARK 210 PH : 6.7; 6.7 REMARK 210 IONIC STRENGTH : 100 MM; 100 MM REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DUPLEX: 20 MM SODIUM REMARK 210 PHOSPHATE (PH 6.7); 56 MM REMARK 210 NACL; 50 UM SODIUM AZIDE; 1 MM REMARK 210 DUPLEX: 20 MM SODIUM PHOSPHATE REMARK 210 (PH 6.7); 56 MM NACL; 50 UM REMARK 210 SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, 2D ROESY, REMARK 210 EXCHANGE-ONLY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, MORASS 2.51 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 11 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : 10 STRUCTURES AND THEIR REMARK 210 MINIMIZED AVERAGE WERE REMARK 210 DEPOSITED 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 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 2 DC A 1 C5' DC A 1 C4' 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 1 DC A 1 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 4 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DC A 5 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DC B 12 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC B 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DG B 18 N3 - C2 - N2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA B 19 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA B 19 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC B 21 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC A 1 C3' - C2' - C1' ANGL. DEV. = 7.3 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DG A 2 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG A 2 N3 - C2 - N2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 3 N3 - C4 - C5 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DT A 4 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DT A 4 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DT A 4 C5 - C4 - O4 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DG A 3 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 2 DC A 5 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 5 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DA A 6 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 2 DA A 6 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DC A 7 N3 - C4 - N4 ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DC A 7 C5 - C4 - N4 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DA A 9 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DA A 9 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DA A 9 N1 - C6 - N6 ANGL. DEV. = -6.6 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DC B 13 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC B 15 N3 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC B 15 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DT B 14 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 2 DG B 16 O4' - C1' - C2' ANGL. DEV. = 4.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 251 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 8 0.07 SIDE_CHAIN REMARK 500 1 DG B 18 0.11 SIDE_CHAIN REMARK 500 2 DG A 3 0.10 SIDE_CHAIN REMARK 500 2 DT A 4 0.10 SIDE_CHAIN REMARK 500 2 DC A 5 0.12 SIDE_CHAIN REMARK 500 2 DA A 6 0.06 SIDE_CHAIN REMARK 500 2 DG A 8 0.07 SIDE_CHAIN REMARK 500 2 DG A 10 0.10 SIDE_CHAIN REMARK 500 2 DG A 11 0.06 SIDE_CHAIN REMARK 500 2 DT B 14 0.10 SIDE_CHAIN REMARK 500 2 DG B 18 0.18 SIDE_CHAIN REMARK 500 3 DC A 1 0.07 SIDE_CHAIN REMARK 500 3 DC A 5 0.10 SIDE_CHAIN REMARK 500 3 DG A 8 0.07 SIDE_CHAIN REMARK 500 3 DG B 18 0.08 SIDE_CHAIN REMARK 500 3 DA B 19 0.09 SIDE_CHAIN REMARK 500 3 DG B 22 0.12 SIDE_CHAIN REMARK 500 4 DT A 4 0.07 SIDE_CHAIN REMARK 500 4 DG A 8 0.08 SIDE_CHAIN REMARK 500 4 DG A 11 0.08 SIDE_CHAIN REMARK 500 4 DC B 12 0.08 SIDE_CHAIN REMARK 500 4 DG B 18 0.09 SIDE_CHAIN REMARK 500 4 DG B 22 0.07 SIDE_CHAIN REMARK 500 5 DG A 2 0.05 SIDE_CHAIN REMARK 500 5 DG A 3 0.07 SIDE_CHAIN REMARK 500 5 DT A 4 0.08 SIDE_CHAIN REMARK 500 5 DA A 6 0.06 SIDE_CHAIN REMARK 500 5 DG A 8 0.09 SIDE_CHAIN REMARK 500 5 DG A 11 0.08 SIDE_CHAIN REMARK 500 5 DC B 15 0.09 SIDE_CHAIN REMARK 500 5 DG B 18 0.13 SIDE_CHAIN REMARK 500 5 DG B 22 0.07 SIDE_CHAIN REMARK 500 6 DT A 4 0.07 SIDE_CHAIN REMARK 500 6 DG A 8 0.08 SIDE_CHAIN REMARK 500 6 DA A 9 0.06 SIDE_CHAIN REMARK 500 6 DC B 15 0.07 SIDE_CHAIN REMARK 500 6 DG B 18 0.13 SIDE_CHAIN REMARK 500 6 DC B 21 0.11 SIDE_CHAIN REMARK 500 7 DG B 18 0.12 SIDE_CHAIN REMARK 500 8 DT A 4 0.10 SIDE_CHAIN REMARK 500 8 DG A 8 0.08 SIDE_CHAIN REMARK 500 8 DA A 9 0.06 SIDE_CHAIN REMARK 500 8 DG B 18 0.14 SIDE_CHAIN REMARK 500 8 DG B 22 0.06 SIDE_CHAIN REMARK 500 9 DG A 2 0.06 SIDE_CHAIN REMARK 500 9 DC A 5 0.06 SIDE_CHAIN REMARK 500 9 DC A 7 0.10 SIDE_CHAIN REMARK 500 9 DA A 9 0.06 SIDE_CHAIN REMARK 500 9 DG A 11 0.07 SIDE_CHAIN REMARK 500 9 DG B 18 0.13 SIDE_CHAIN REMARK 500 10 DC A 7 0.09 SIDE_CHAIN REMARK 500 10 DG A 8 0.09 SIDE_CHAIN REMARK 500 10 DA A 9 0.05 SIDE_CHAIN REMARK 500 10 DG A 11 0.06 SIDE_CHAIN REMARK 500 10 DC B 15 0.08 SIDE_CHAIN REMARK 500 10 DG B 16 0.06 SIDE_CHAIN REMARK 500 10 DG B 18 0.11 SIDE_CHAIN REMARK 500 10 DC B 20 0.06 SIDE_CHAIN REMARK 500 10 DC B 21 0.08 SIDE_CHAIN REMARK 500 11 DG B 18 0.10 SIDE_CHAIN REMARK 500 11 DC B 21 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 TBC A 23 DBREF 1N8C A 1 11 PDB 1N8C 1N8C 1 11 DBREF 1N8C B 12 22 PDB 1N8C 1N8C 12 22 SEQRES 1 A 11 DC DG DG DT DC DA DC DG DA DG DG SEQRES 1 B 11 DC DC DT DC DG DT DG DA DC DC DG HET TBC A 23 36 HETNAM TBC (9S,10R)-9-HYDROXY-7,8,9,10-TETRAHYDROBENZO[A]PYRENE FORMUL 3 TBC C20 H16 O LINK N6 DA A 6 C10 TBC A 23 1555 1555 1.38 SITE 1 AC1 5 DC A 5 DA A 6 DC A 7 DT B 17 SITE 2 AC1 5 DG B 18 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 224 0 1 0 0 0 2 6 0 0 0 2 END