1n5c: Difference between revisions
New page: left|200px<br /><applet load="1n5c" size="450" color="white" frame="true" align="right" spinBox="true" caption="1n5c, resolution 1.79Å" /> '''Crystal Structure An... |
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[[Image:1n5c.gif|left|200px]]<br /><applet load="1n5c" size=" | [[Image:1n5c.gif|left|200px]]<br /><applet load="1n5c" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1n5c, resolution 1.79Å" /> | caption="1n5c, resolution 1.79Å" /> | ||
'''Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG'''<br /> | '''Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG'''<br /> | ||
==Overview== | ==Overview== | ||
Exocyclic DNA adducts are formed from metabolites of chemical carcinogens | 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== | ==About this Structure== | ||
1N5C is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | 1N5C is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N5C OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Fernandes, A.]] | [[Category: Fernandes, A.]] | ||
[[Category: Freisinger, E.]] | [[Category: Freisinger, E.]] | ||
[[Category: Grollman, A | [[Category: Grollman, A P.]] | ||
[[Category: Kisker, C | [[Category: Kisker, C F.]] | ||
[[Category: NA]] | [[Category: NA]] | ||
[[Category: 3]] | [[Category: 3]] | ||
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[[Category: n4-etheno-2'-cytidine modification opposite g]] | [[Category: n4-etheno-2'-cytidine modification opposite g]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:02:25 2008'' | ||
Revision as of 15:02, 21 February 2008
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Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG
OverviewOverview
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 StructureAbout this Structure
1N5C is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
ReferenceReference
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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