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| - | [[Image:1y6t.gif|left|200px]] | |
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| - | <!--
| + | ==HIV-1 Dis(Mal) Duplex Co Hexamine-Soaked== |
| - | The line below this paragraph, containing "STRUCTURE_1y6t", creates the "Structure Box" on the page.
| + | <StructureSection load='1y6t' size='340' side='right'caption='[[1y6t]], [[Resolution|resolution]] 2.60Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1y6t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y6T 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]] 2.6Å</td></tr> |
| - | --> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3CO:COBALT+(III)+ION'>3CO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | {{STRUCTURE_1y6t| PDB=1y6t | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1y6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6t OCA], [https://pdbe.org/1y6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y6t RCSB], [https://www.ebi.ac.uk/pdbsum/1y6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y6t ProSAT]</span></td></tr> |
| | + | </table> |
| | | | |
| - | '''HIV-1 Dis(Mal) Duplex Co Hexamine-Soaked'''
| + | ==See Also== |
| - | | + | *[[Ecotin|Ecotin]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | Metal ions, and magnesium in particular, are known to be involved in RNA folding by stabilizing secondary and tertiary structures, and, as cofactors, in RNA enzymatic activity. We have conducted a systematic crystallographic analysis of cation binding to the duplex form of the HIV-1 RNA dimerization initiation site for the subtype-A and -B natural sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+, Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)6]3+ and [Ru (NH3)6]3+ were found to bind to the DIS duplex structure. Although the two sequences are very similar, strong differences were found in their cation binding properties. Divalent cations bind almost exclusively, as Mg2+, at 'Hoogsteen' sites of guanine residues, with a cation-dependent affinity for each site. Notably, a given cation can have very different affinities for a priori equivalent sites within the same molecule. Surprisingly, none of the two hexammines used were able to efficiently replace hexahydrated magnesium. Instead, [Co (NH3)4]3+ was seen bound by inner-sphere coordination to the RNA. This raises some questions about the practical use of [Co (NH3)6]3+ as a [Mg (H2O)6]2+ mimetic. Also very unexpected was the binding of the small Au3+ cation exactly between the Watson-Crick sites of a G-C base pair after an obligatory deprotonation of N1 of the guanine base. This extensive study of metal ion binding using X-ray crystallography significantly enriches our knowledge on the binding of middleweight or heavy metal ions to RNA, particularly compared with magnesium.
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Dumas P]] |
| - | ==About this Structure==
| + | [[Category: Ennifar E]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6T OCA].
| + | [[Category: Walter P]] |
| - | | + | |
| - | ==Reference==
| + | |
| - | A crystallographic study of the binding of 13 metal ions to two related RNA duplexes., Ennifar E, Walter P, Dumas P, Nucleic Acids Res. 2003 May 15;31(10):2671-82. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12736317 12736317]
| + | |
| - | [[Category: Dumas, P.]] | + | |
| - | [[Category: Ennifar, E.]] | + | |
| - | [[Category: Walter, P.]] | + | |
| - | [[Category: Hiv-1]]
| + | |
| - | [[Category: Metal ion]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 15:56:33 2008''
| + | |
