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[[Image:1n5c.gif|left|200px]]


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==Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG==
The line below this paragraph, containing "STRUCTURE_1n5c", creates the "Structure Box" on the page.
<StructureSection load='1n5c' size='340' side='right'caption='[[1n5c]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1n5c]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N5C FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.79&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDC:N3,N4-ETHENO-2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>EDC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
{{STRUCTURE_1n5c|  PDB=1n5c  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n5c OCA], [https://pdbe.org/1n5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n5c RCSB], [https://www.ebi.ac.uk/pdbsum/1n5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n5c ProSAT]</span></td></tr>
 
</table>
'''Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Fernandes A]]
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.
[[Category: Freisinger E]]
 
[[Category: Grollman AP]]
==About this Structure==
[[Category: Kisker CF]]
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N5C 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:[http://www.ncbi.nlm.nih.gov/pubmed/12787670 12787670]
[[Category: Fernandes, A.]]
[[Category: Freisinger, E.]]
[[Category: Grollman, A P.]]
[[Category: Kisker, C F.]]
[[Category: 3,n4-etheno-2'-cytidine modification opposite g]]
[[Category: B form double helix]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 02:06:55 2008''

Latest revision as of 10:52, 14 February 2024

Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCGCrystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG

Structural highlights

1n5c is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.79Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1n5c, resolution 1.79Å

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