10 20 30 40 50 60 70 80 2KAR - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 13-NOV-08 2KAR
TITLE HNE-DG ADDUCT MISMATCHED WITH DA IN ACIDIC 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 2KAR 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 2KAR 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 RCSB100889.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM DNA 5'-D(*DGP*DCP*DTP* REMARK 210 DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3', 1.0 MM 5'-D(*DGP*DGP* REMARK 210 DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3', 1.0 MM (2E,4R)-4- REMARK 210 HYDROXYNON-2-ENAL, 90% H2O/10% 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 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 1 C2 DG A 1 N3 0.062 REMARK 500 DG A 1 N3 DG A 1 C4 0.064 REMARK 500 DG A 1 N7 DG A 1 C8 0.100 REMARK 500 DA A 4 N1 DA A 4 C2 0.071 REMARK 500 DA A 4 C2 DA A 4 N3 0.077 REMARK 500 DA A 4 N3 DA A 4 C4 0.063 REMARK 500 DA A 4 C6 DA A 4 N1 0.046 REMARK 500 DA A 4 N7 DA A 4 C8 0.101 REMARK 500 DG A 5 C2 DG A 5 N3 0.064 REMARK 500 DG A 5 N3 DG A 5 C4 0.063 REMARK 500 DG A 5 N7 DG A 5 C8 0.099 REMARK 500 DG A 7 C2 DG A 7 N3 0.065 REMARK 500 DG A 7 N3 DG A 7 C4 0.058 REMARK 500 DG A 7 N7 DG A 7 C8 0.095 REMARK 500 DA A 8 N1 DA A 8 C2 0.070 REMARK 500 DA A 8 C2 DA A 8 N3 0.076 REMARK 500 DA A 8 N3 DA A 8 C4 0.062 REMARK 500 DA A 8 C6 DA A 8 N1 0.043 REMARK 500 DA A 8 N7 DA A 8 C8 0.101 REMARK 500 DG A 9 C2 DG A 9 N3 0.064 REMARK 500 DG A 9 N3 DG A 9 C4 0.063 REMARK 500 DG A 9 N7 DG A 9 C8 0.097 REMARK 500 DG B 13 C2 DG B 13 N3 0.063 REMARK 500 DG B 13 N3 DG B 13 C4 0.065 REMARK 500 DG B 13 N7 DG B 13 C8 0.100 REMARK 500 DG B 14 C2 DG B 14 N3 0.063 REMARK 500 DG B 14 N3 DG B 14 C4 0.063 REMARK 500 DG B 14 N7 DG B 14 C8 0.101 REMARK 500 DA B 15 N1 DA B 15 C2 0.071 REMARK 500 DA B 15 C2 DA B 15 N3 0.080 REMARK 500 DA B 15 N3 DA B 15 C4 0.061 REMARK 500 DA B 15 N7 DA B 15 C8 0.098 REMARK 500 DA B 18 N1 DA B 18 C2 0.068 REMARK 500 DA B 18 C2 DA B 18 N3 0.073 REMARK 500 DA B 18 N3 DA B 18 C4 0.058 REMARK 500 DA B 18 N7 DA B 18 C8 0.101 REMARK 500 DA B 18 C6 DA B 18 N6 0.053 REMARK 500 DG B 19 C2 DG B 19 N3 0.060 REMARK 500 DG B 19 N3 DG B 19 C4 0.061 REMARK 500 DG B 19 N7 DG B 19 C8 0.101 REMARK 500 DA B 22 N1 DA B 22 C2 0.071 REMARK 500 DA B 22 C2 DA B 22 N3 0.076 REMARK 500 DA B 22 N3 DA B 22 C4 0.062 REMARK 500 DA B 22 C6 DA B 22 N1 0.044 REMARK 500 DA B 22 N7 DA B 22 C8 0.101 REMARK 500 DG B 23 C2 DG B 23 N3 0.063 REMARK 500 DG B 23 N3 DG B 23 C4 0.063 REMARK 500 DG B 23 N7 DG B 23 C8 0.101 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG A 1 N3 - C4 - C5 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 1 N9 - C4 - C5 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 2 OP1 - P - OP2 ANGL. DEV. = -14.2 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT A 3 OP1 - P - OP2 ANGL. DEV. = -14.3 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT A 3 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA A 4 OP1 - P - OP2 ANGL. DEV. = -14.6 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA A 4 N1 - C2 - N3 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA A 4 C2 - N3 - C4 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DA A 4 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 5 OP1 - P - OP2 ANGL. DEV. = -14.4 DEGREES REMARK 500 DG A 5 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG A 5 N9 - C4 - C5 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC A 6 OP1 - P - OP2 ANGL. DEV. = -14.0 DEGREES REMARK 500 DC A 6 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG A 7 OP1 - P - OP2 ANGL. DEV. = -14.7 DEGREES REMARK 500 DG A 7 N3 - C4 - C5 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG A 7 N9 - C4 - C5 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 7 N3 - C2 - N2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA A 8 OP1 - P - OP2 ANGL. DEV. = -13.6 DEGREES REMARK 500 DA A 8 N1 - C2 - N3 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA A 8 C2 - N3 - C4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA A 8 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG A 9 OP1 - P - OP2 ANGL. DEV. = -14.6 DEGREES REMARK 500 DG A 9 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG A 9 N9 - C4 - C5 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT A 10 OP1 - P - OP2 ANGL. DEV. = -14.4 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT A 10 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC A 11 OP1 - P - OP2 ANGL. DEV. = -13.9 DEGREES REMARK 500 DC A 11 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC A 12 OP1 - P - OP2 ANGL. DEV. = -14.6 DEGREES REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC A 12 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -6.1 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG B 13 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG B 13 N9 - C4 - C5 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 14 OP1 - P - OP2 ANGL. DEV. = -14.6 DEGREES REMARK 500 DG B 14 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG B 14 N9 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 89 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 DG A 7 0.07 SIDE_CHAIN REMARK 500 DC A 12 0.06 SIDE_CHAIN 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: 2KAS RELATED DB: PDB
DBREF 2KAR A 1 12 PDB 2KAR 2KAR 1 12 DBREF 2KAR B 13 24 PDB 2KAR 2KAR 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 1.46 LINK N1 DG A 7 C1 HND A 25 1555 1555 1.49
SITE 1 AC1 4 DG A 5 DC A 6 DG A 7 DC B 16
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