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| | <StructureSection load='1icg' size='340' side='right'caption='[[1icg]], [[Resolution|resolution]] 1.53Å' scene=''> | | <StructureSection load='1icg' size='340' side='right'caption='[[1icg]], [[Resolution|resolution]] 1.53Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1icg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ICG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ICG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1icg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ICG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ICG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.53Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UFP:5-FLUORO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>UFP</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene>, <scene name='pdbligand=UFP:5-FLUORO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>UFP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[165d|165d]]</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=1icg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1icg OCA], [https://pdbe.org/1icg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1icg RCSB], [https://www.ebi.ac.uk/pdbsum/1icg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1icg ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1icg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1icg OCA], [http://pdbe.org/1icg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1icg RCSB], [http://www.ebi.ac.uk/pdbsum/1icg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1icg ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cruse, W]] | + | [[Category: Cruse W]] |
| - | [[Category: Neuman, A]] | + | [[Category: Neuman A]] |
| - | [[Category: Prange, T]] | + | [[Category: Prange T]] |
| - | [[Category: Saludjian, P]] | + | [[Category: Saludjian P]] |
| - | [[Category: C-u mismatch]]
| + | |
| - | [[Category: Dna-rna complex]]
| + | |
| - | [[Category: Fluoro-uracil]]
| + | |
| - | [[Category: G-u mismatch]]
| + | |
| - | [[Category: Iridium hexammine]]
| + | |
| - | [[Category: Rhodium hexammine]]
| + | |
| - | [[Category: Rna/dna hybrid]]
| + | |
| Structural highlights
Publication Abstract from PubMed
In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-d(X)U (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G-U and C-U mismatches. The deoxy chloro- and bromouracil derivatives are isomorphous, space group C2, unit-cell parameters a = 53.80, b = 19.40, c = 50.31 A, beta = 109.9 degrees, with the same infinite helix arrangement in the packing along the c axis with one extra DNA halogenouracil base included in the stacking. However, the fluorouracil derivative, with unit-cell parameters a = 53.75, b = 19.40, c = 45.84 A, beta = 105.7 degrees, is not isomorphous. The corresponding extra DNA base d(F)U of the second strand is ejected out of the helical stack, leading to a shortening of the c axis. The specific destabilization of the fluorouracil for the duplex building is analyzed in terms of the polarization effect of the halogen atom attached to the 3'-terminal base that modulates its interactions.
Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues.,Cruse W, Saludjian P, Neuman A, Prange T Acta Crystallogr D Biol Crystallogr. 2001 Nov;57(Pt 11):1609-13. Epub 2001, Oct 25. PMID:11679725[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Cruse W, Saludjian P, Neuman A, Prange T. Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues. Acta Crystallogr D Biol Crystallogr. 2001 Nov;57(Pt 11):1609-13. Epub 2001, Oct 25. PMID:11679725
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