1g5d | pdb_00001g5d

NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA ANOMER

spinqualitylabelsall models 1g5d, 10 NMR models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1g5d is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ORP Related: 1a9i, 1a9j, 1giz, 1g5e, 1gj0 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum Publication Abstract from PubMed The antitumor antibiotic bleomycin causes two major lesions in the deoxyribose backbone of DNA: formation of 4'-keto abasic sites and formation of strand breaks with 3'-phosphoglycolate and 5'-phosphate ends. As a model for the 4'-keto abasic site, we have characterized an abasic site (X) in d(CCAAAGXACTGGG).d(CCCAGTACTTTGG) by two-dimensional NMR spectroscopy. A total of 475 NOEs and 101 dihedral angles provided the restraints for molecular modeling. Four unusual NOEs were observed between each anomer of the abasic site and the neighboring bases. In addition, four coupling constants for adjacent protons of the deoxyribose of both the alpha and beta anomers of the abasic site were observed. The modeling suggests that for both anomers the abasic site is extrahelical, without significant distortion of the backbone opposite the lesion. The coupling constants further allowed assignment of an unusual sugar pucker for each anomer. The unique position of the abasic site in our structural model for each anomer is discussed in terms of repair of such lesions in vivo. Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation.,Hoehn ST, Turner CJ, Stubbe J Nucleic Acids Res. 2001 Aug 15;29(16):3413-23. PMID:11504879 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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