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1icg

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(New page: 200px<br /><applet load="1icg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1icg, resolution 1.53&Aring;" /> '''STRUCTURE OF THE HYB...)
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[[Image:1icg.gif|left|200px]]<br /><applet load="1icg" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1icg, resolution 1.53&Aring;" />
 
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'''STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF IR(NH3)6+++'''<br />
 
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==Overview==
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==STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF IR(NH3)6+++==
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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.
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<StructureSection load='1icg' size='340' side='right'caption='[[1icg]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.53&#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=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>
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<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>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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<ref>PMID:11679725</ref>
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1ICG is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CL and IRI as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ICG OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11679725 11679725]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1icg" style="background-color:#fffaf0;"></div>
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[[Category: Cruse, W.]]
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== References ==
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[[Category: Neuman, A.]]
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<references/>
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[[Category: Prange, T.]]
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__TOC__
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[[Category: Saludjian, P.]]
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</StructureSection>
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[[Category: CL]]
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[[Category: Large Structures]]
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[[Category: IRI]]
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[[Category: Cruse W]]
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[[Category: c-u mismatch]]
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[[Category: Neuman A]]
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[[Category: fluoro-uracil]]
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[[Category: Prange T]]
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[[Category: g-u mismatch]]
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[[Category: Saludjian P]]
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[[Category: iridium hexammine]]
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[[Category: rhodium hexammine]]
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[[Category: rna/dna hybrid]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 21:46:21 2007''
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STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF IR(NH3)6+++

PDB ID 1icg

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