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| [[Image:1n5c.gif|left|200px]]
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| {{Structure
| | ==Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG== |
| |PDB= 1n5c |SIZE=350|CAPTION= <scene name='initialview01'>1n5c</scene>, resolution 1.79Å
| | <StructureSection load='1n5c' size='340' side='right'caption='[[1n5c]], [[Resolution|resolution]] 1.79Å' scene=''> |
| |SITE=
| | == Structural highlights == |
| |LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene>
| | <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> |
| |ACTIVITY=
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.79Å</td></tr> |
| |GENE=
| | <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> |
| }}
| | <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]] |
| 1N5C is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N5C OCA].
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| ==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]
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| [[Category: Protein complex]] | |
| [[Category: Fernandes, A.]] | |
| [[Category: Freisinger, E.]] | |
| [[Category: Grollman, A P.]] | |
| [[Category: Kisker, C F.]] | |
| [[Category: NA]] | |
| [[Category: 3]] | |
| [[Category: b form double helix]] | |
| [[Category: n4-etheno-2'-cytidine modification opposite g]] | |
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:52:27 2008''
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