10 20 30 40 50 60 70 80 1AGU - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 25-MAR-97 1AGU
TITLE THE SOLUTION NMR STRUCTURE OF THE C10R ADDUCT OF TITLE 2 BENZO[A]PYRENE-DIOL-EPOXIDE AT THE N6 POSITION OF ADENINE TITLE 3 OF AN 11 BASE-PAIR OLIGONUCLEOTIDE SEQUENCE CODING FOR TITLE 4 AMINO ACIDS 60-62 OF THE PRODUCT OF THE N-RAS TITLE 5 PROTOONCOGENE, MINIMIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*GP*AP*CP*EP*AP*GP*AP*AP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: C10R-BPDE-N6-ADENINE ADDUCT; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: C10R-BPDE-N6-ADENINE ADDUCT
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS DNA DUPLEX, HUMAN N-RAS GENE, CODON 61 SEQUENCE, C10R-BPDE KEYWDS 2 ADDUCT, INTERCALATION, N6-ADENINE ADDUCT, DEOXYRIBONUCLEIC KEYWDS 3 ACID
EXPDTA SOLUTION NMR
AUTHOR I.S.ZEGAR,M.P.STONE
REVDAT 2 24-FEB-09 1AGU 1 VERSN REVDAT 1 20-AUG-97 1AGU 0
JRNL AUTH I.S.ZEGAR,S.J.KIM,T.N.JOHANSEN,P.J.HORTON, JRNL AUTH 2 C.M.HARRIS,T.M.HARRIS,M.P.STONE JRNL TITL ADDUCTION OF THE HUMAN N-RAS CODON 61 SEQUENCE JRNL TITL 2 WITH (-)-(7S,8R,9R,10S)-7,8-DIHYDROXY-9,10-EPOXY-7, JRNL TITL 3 8,9,10-TETRAHYDROBENZO[A] PYRENE: STRUCTURAL JRNL TITL 4 REFINEMENT OF THE INTERCALATED SRSR(61,2) JRNL TITL 5 (-)-(7S,8R,9S,1 0R)-N6-[10-(7,8,9,10- JRNL TITL 6 TETRAHYDROBENZO[A]PYRENYL)]-2'-DEOXYADENOSYL JRNL TITL 7 ADDUCT FROM 1H NMR JRNL REF BIOCHEMISTRY V. 35 6212 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8639561 JRNL DOI 10.1021/BI9524732
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.FENG,M.P.STONE REMARK 1 TITL SOLUTION STRUCTURE OF AN OLIGODEOXYNUCLEOTIDE REMARK 1 TITL 2 CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE REMARK 1 TITL 3 REFINED FROM 1H NMR USING MOLECULAR DYNAMICS REMARK 1 TITL 4 RESTRAINED BY NUCLEAR OVERHAUSER EFFECTS REMARK 1 REF CHEM.RES.TOXICOL. V. 8 821 1995 REMARK 1 REFN ISSN 0893-228X
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE.
REMARK 4 REMARK 4 1AGU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, 2QF-COSY, AND TOCSY, : REMARK 210 NOESY, H REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, X-PLOR, MARDIGRAS, REMARK 210 CORMA REMARK 210 METHOD USED : NOE-RESTRAINED MOLECULAR REMARK 210 DYNAMICS/SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : THIS STRUCTURE PROVIDED THE REMARK 210 BEST-FIT FOR THE NOE DATA REMARK 210 BASED ON THE RELAXATION MATRIX REMARK 210 ANALYSIS USING CORMA. 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 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 2 O5' DG A 2 C5' -0.207 REMARK 500 DG A 11 N7 DG A 11 C8 -0.039 REMARK 500 DG B 18 P DG B 18 OP1 -0.445 REMARK 500 DG B 18 P DG B 18 OP2 -0.431 REMARK 500 DT B 17 O3' DG B 18 P -0.306 REMARK 500 DT B 19 O5' DT B 19 C5' -0.219 REMARK 500 DG B 22 N7 DG B 22 C8 -0.041 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 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT B 17 C3' - O3' - P ANGL. DEV. = 11.9 DEGREES REMARK 500 DG B 18 O3' - P - O5' ANGL. DEV. = 14.5 DEGREES REMARK 500 DT B 19 O5' - C5' - C4' ANGL. DEV. = 16.1 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL
DBREF 1AGU A 1 11 PDB 1AGU 1AGU 1 11 DBREF 1AGU B 12 22 PDB 1AGU 1AGU 12 22
SEQRES 1 A 11 DC DG DG DA DC E DA DG DA DA DG SEQRES 1 B 11 DC DT DT DC DT DT DG DT DC DC DG
MODRES 1AGU E A 6 DA
HET E A 6 69
HETNAM E N-((-)-(7S,8R,9S,10R)[7,8,9-TRIHYDROXY-7,8,9,10-TETRA HETNAM 2 E HYDROBENZO[A]PYREN-10-YL])-2'-DEOXY-ADENOSINE-5'- HETNAM 3 E MONOPHOSPHATE
FORMUL 1 E C30 H28 N5 O9 P
LINK P E A 6 O3' DC A 5 1555 1555 1.61 LINK O3' E A 6 P DA A 7 1555 1555 1.61
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