2KAS - Header Asymmetric Unit

HEADER DNA 13-NOV-08 2KAS

TITLE HNE-DG ADDUCT MISMATCHED WITH DA IN BASIC SOLUTION

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*DAP*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: THE DNA OLIGOMER IS CHEMICALLY SYNTHESIZED.; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: THE DNA OLIGOMER IS CHEMICALLY SYNTHESIZED.

KEYWDS HNE-DG, MISMATCH, HYDROXYNONENAL, DNA

EXPDTA SOLUTION NMR

AUTHOR H.HUANG,H.WANG,R.S.LLOYD,C.J.RIZZO,M.P.STONE

REVDAT 1 26-MAY-09 2KAS 0

JRNL AUTH H.HUANG,H.WANG,R.S.LLOYD,C.J.RIZZO,M.P.STONE JRNL TITL CONFORMATIONAL INTERCONVERSION OF THE JRNL TITL 2 TRANS-4-HYDROXYNONENAL-DERIVED (6S,8R,11S) JRNL TITL 3 1,N(2)-DEOXYGUANOSINE ADDUCT WHEN MISMATCHED WITH JRNL TITL 4 DEOXYADENOSINE IN DNA JRNL REF CHEM.RES.TOXICOL. V. 22 187 2009 JRNL REFN ISSN 0893-228X JRNL PMID 19053179 JRNL DOI 10.1021/TX800320M

REMARK 1

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 KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 2KAS COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-08. REMARK 100 THE RCSB ID CODE IS RCSB100890.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 8.9 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM DNA (5'-D(*DGP*DCP* REMARK 210 DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'), 1.0 MM DNA (5'- REMARK 210 D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3'), 1.0 MM REMARK 210 (2E,4R)-4-HYDROXYNON-2-ENAL, 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 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 6 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 7 C6 - N1 - C2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG A 7 N3 - C2 - N2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -6.1 DEGREES REMARK 500 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA B 18 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 18 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA B 18 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 DT B 17 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DC B 20 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 20 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA B 22 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 22 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC B 24 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 24 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL

REMARK 600 REMARK 600 HETEROGEN REMARK 600 THE LIGAND HND FORMS TWO COVALENT BONDS WITH THE DEOXY-GUANINE REMARK 600 AT POSITION 7 OF CHAIN A. THIS LIGAND IS FORMED BY CHEMICAL REMARK 600 REACTION OF ANOTHER LIGAND HNE.

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HND A 25

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KAR RELATED DB: PDB

DBREF 2KAS A 1 12 PDB 2KAS 2KAS 1 12 DBREF 2KAS B 13 24 PDB 2KAS 2KAS 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 DA DG DC DT DA DG DC

HET HND A 25 29

HETNAM HND (4S)-NONANE-1,4-DIOL

FORMUL 3 HND C9 H20 O2

LINK N2 DG A 7 C3 HND A 25 1555 1555 1.45 LINK N1 DG A 7 C1 HND A 25 1555 1555 1.49

SITE 1 AC1 5 DG A 7 DA A 8 DG A 9 DA B 18 SITE 2 AC1 5 DG B 19

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