10 20 30 40 50 60 70 80 2K8T - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 23-SEP-08 2K8T
TITLE SOLUTION NMR STRUCTURE OF TRANS-4-HYDROXYNONENAL DERIVED DG TITLE 2 ADDUCT OF (6R,8S,11R)-CONFIGURATION OPPOSITE DC
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'- COMPND 8 D(*DGP*DGP*DAP*DCP*DTP*DCP*DGP*DCP*DTP*DAP*DGP*DC)-3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DNA STRAND A; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: DNA STRAND B
KEYWDS HNE-DG (6R,8S,11R), HNE DERIVED DG ADDUCT, TRANS-4- KEYWDS 2 HYDROXYNONENAL, DNA
EXPDTA SOLUTION NMR
AUTHOR H.HUANG,H.WANG,N.QI,R.S.LLOYD,C.J.RIZZO,M.P.STONE
REVDAT 3 24-FEB-09 2K8T 1 VERSN REVDAT 2 11-NOV-08 2K8T 1 JRNL REVDAT 1 04-NOV-08 2K8T 0
JRNL AUTH H.HUANG,H.WANG,N.QI,R.S.LLOYD,C.J.RIZZO,M.P.STONE JRNL TITL THE STEREOCHEMISTRY OF JRNL TITL 2 TRANS-4-HYDROXYNONENAL-DERIVED EXOCYCLIC JRNL TITL 3 1,N2-2'-DEOXYGUANOSINE ADDUCTS MODULATES FORMATION JRNL TITL 4 OF INTERSTRAND CROSS-LINKS IN THE 5'-CPG-3' JRNL TITL 5 SEQUENCE. JRNL REF BIOCHEMISTRY V. 47 11457 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18847226 JRNL DOI 10.1021/BI8011143
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2K8T COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-08. REMARK 100 THE RCSB ID CODE IS RCSB100820.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DNA (5'-D(*DGP*DCP*DTP* REMARK 210 DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'), 1 MM DNA (5'-D(*DGP* REMARK 210 DGP*DAP*DCP*DTP*DCP*DGP*DCP*DTP*DAP*DGP*DC)-3'), 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM 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 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 2 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC A 6 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT A 10 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 18 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC B 18 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC B 20 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 22 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 22 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC B 24 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 24 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES 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 DG A 7 0.06 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 HNB A 125
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K8U RELATED DB: PDB REMARK 900 TRANS-4-HYDROXYNONENAL DERIVED DG ADDUCT OF (6S,8R,11S)- REMARK 900 CONFIGURATION MATCHED WITH DC
DBREF 2K8T A 1 12 PDB 2K8T 2K8T 1 12 DBREF 2K8T B 13 24 PDB 2K8T 2K8T 13 24
SEQRES 1 A 12 DG DC DT DA DG DC DG DA DG DT DC DC SEQRES 1 B 12 DG DG DA DC DT DC DG DC DT DA DG DC
HET HNB A 125 28
HETNAM HNB (2S,5R)-5-PENTYLTETRAHYDROFURAN-2-OL
FORMUL 3 HNB C9 H18 O2
LINK N2 DG A 7 C3 HNB A 125 1555 1555 1.48
SITE 1 AC1 5 DG A 7 DA A 8 DG A 9 DG B 19 SITE 2 AC1 5 DC B 20
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