1u6c | pdb_00001u6c

The NMR-derived solution structure of the (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide

spinqualitylabelsall models 1u6c Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1u6c is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Solution NMR Ligands: 2BU Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed The solution structure of the (2S,3S)-N(6)-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl adduct arising from the alkylation of adenine N(6) at position X(6) in d(CGGACXAGAAG).d(CTTCTTGTCCG), by butadiene diol epoxide, was determined. This oligodeoxynucleotide contains codon 61 (underlined) of the human N-ras protooncogene. This oligodeoxynucleotide, containing the adenine N(6) adduct butadiene triol (BDT) adduct at the second position of codon 61, was named the ras61 S,S-BDT-(61,2) adduct. NMR spectroscopy revealed modest structural perturbations localized to the site of adduction at X(6).T(17), and its nearest-neighbor base pairs C(5).G(18) and A(7).T(16). All sequential NOE connectivities arising from DNA protons were observed. Torsion angle analysis from COSY data suggested that the deoxyribose sugar at X(6) remained in the C2'-endo conformation. Molecular dynamics calculations using a simulated annealing protocol restrained by a total of 442 NOE-derived distances and J coupling-derived torsion angles refined structures in which the BDT moiety oriented in the major groove. Relaxation matrix analysis suggested hydrogen bonding between the hydroxyl group located at the beta-carbon of the BDT moiety and the T(17) O(4) of the modified base pair X(6).T(17). The minimal perturbation of DNA induced by this major groove adduct correlated with its facile bypass by three Escherichia coli DNA polymerases in vitro and its weak mutagenicity [Carmical, J. R., Nechev, L. V., Harris, C. M., Harris, T. M., and Lloyd, R. S. (2000) Environ. Mol. Mutagen. 35, 48-56]. Overall, the structure of this adduct is consistent with an emerging pattern in which major groove adenine N(6) alkylation products of styrene and butadiene oxides that do not strongly perturb DNA structure are not strongly mutagenic. Structure of a site specific major groove (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide.,Scholdberg TA, Nechev LV, Merritt WK, Harris TM, Harris CM, Lloyd RS, Stone MP Chem Res Toxicol. 2004 Jun;17(6):717-30. PMID:15206893 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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