3zp8

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{{STRUCTURE_3zp8| PDB=3zp8 | SCENE= }}
 
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===HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME===
 
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{{ABSTRACT_PUBMED_23711504}}
 
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==About this Structure==
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==HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME==
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[[3zp8]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3zd3 3zd3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZP8 OCA].
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<StructureSection load='3zp8' size='340' side='right'caption='[[3zp8]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3zp8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3zd3 3zd3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZP8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZP8 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]] 1.55&#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=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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=3zp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zp8 OCA], [https://pdbe.org/3zp8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zp8 RCSB], [https://www.ebi.ac.uk/pdbsum/3zp8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zp8 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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We have obtained a 1.55-A crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni under conditions that permit detailed observations of Na+ ion binding in the ribozyme's active site. At least two such Na+ ions are observed. The first Na+ ion binds to the N7 of G10.1 and the adjacent A9 phosphate in a manner identical with that previously observed for divalent cations. A second Na+ ion binds to the Hoogsteen face of G12, the general base in the hammerhead cleavage reaction, thereby potentially dissipating the negative charge of the catalytically active enolate form of the nucleotide base. A potential but more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with that of previous predictions. Hammerhead ribozymes have been observed to be active in the presence of high concentrations of monovalent cations, including Na+, but the mechanism by which monovalent cations substitute for divalent cations in hammerhead catalysis remains unclear. Our results enable us to suggest that Na+ directly and specifically substitutes for divalent cations in the hammerhead active site. The detailed geometry of the pre-catalytic active-site complex is also revealed with a new level of precision, thanks to the quality of the electron density maps obtained from what is currently the highest-resolution ribozyme structure in the Protein Data Bank.
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==See Also==
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Active-Site Monovalent Cations Revealed in a 1.55-A-Resolution Hammerhead Ribozyme Structure.,Anderson M, Schultz EP, Martick M, Scott WG J Mol Biol. 2013 May 25. pii: S0022-2836(13)00331-8. doi:, 10.1016/j.jmb.2013.05.017. PMID:23711504<ref>PMID:23711504</ref>
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*[[Ribozyme|Ribozyme]]
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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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<ref group="xtra">PMID:023711504</ref><references group="xtra"/><references/>
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</div>
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[[Category: Anderson, M.]]
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<div class="pdbe-citations 3zp8" style="background-color:#fffaf0;"></div>
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[[Category: Martick, M.]]
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[[Category: Schultz, E.]]
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==See Also==
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[[Category: Scott, W G.]]
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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[[Category: Catalytic rna]]
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== References ==
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[[Category: Rna]]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Synthetic construct]]
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[[Category: Anderson M]]
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[[Category: Martick M]]
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[[Category: Schultz E]]
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[[Category: Scott WG]]

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HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME

PDB ID 3zp8

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