1n5c
From Proteopedia
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Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG
Overview
Exocyclic DNA adducts are formed from metabolites of chemical carcinogens, and have also been detected as endogenous lesions in human DNA. The, exocyclic adduct 3,N(4)-etheno-2'-deoxycytidine (epsilon dC), positioned, opposite deoxyguanosine in the B-form duplex of the dodecanucleotide, d(CGCGAATTepsilonCGCG), has been crystallographically characterized at, 1.8A resolution. This self-complementary oligomer crystallizes in space, group P3(2)12, containing a single strand in the asymmetric unit. The, crystal structure was solved by isomorphous replacement with the, corresponding unmodified dodecamer structure. Exposure of both structures, to identical crystal packing forces allows a detailed investigation of the, influence of the exocyclic base adduct on the overall helical structure, and local geometry. Structural changes are limited to the epsilon C:G and, adjacent T:A and G:C base-pairs. The standard Watson-Crick base-pairing, scheme, retained in the T:A and G:C base-pairs, is blocked by the etheno, bridge in the epsilon C:G pair. In its place, a hydrogen bond involving O2, of epsilon C and N1 of G is present. Comparison with an epsilon, dC-containing NMR structure confirms the general conformation reported for, epsilon C:G, including the hydrogen bonding features. Superposition with, the crystal structure of a DNA duplex containing a T:G wobble pair shows, similar structural changes imposed by both mismatches. Evaluation of the, hydration shell of the duplex with bond valence calculations reveals two, sodium ions in the crystal.
About this Structure
1N5C is a Protein complex structure of sequences from [1] with NA as ligand. Full crystallographic information is available from OCA.
Reference
Crystallographic characterization of an exocyclic DNA adduct: 3,N4-etheno-2'-deoxycytidine in the dodecamer 5'-CGCGAATTepsilonCGCG-3'., Freisinger E, Fernandes A, Grollman AP, Kisker C, J Mol Biol. 2003 Jun 13;329(4):685-97. PMID:12787670
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