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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=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=EDC:N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>EDC</scene>, <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n5c OCA], [http://www.ebi.ac.uk/pdbsum/1n5c PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1n5c RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG'''
| + | [[Category: Fernandes A]] |
| - | | + | [[Category: Freisinger E]] |
| - | | + | [[Category: Grollman AP]] |
| - | ==Overview==
| + | [[Category: Kisker CF]] |
| - | 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.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 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: 3,n4-etheno-2'-cytidine modification opposite g]]
| + | |
| - | [[Category: b form double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:25:34 2008''
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