1z7f: Difference between revisions

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{{Seed}}
[[Image:1z7f.png|left|200px]]


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==Crystal structure of 16 base pair RNA duplex containing a C-A mismatch==
The line below this paragraph, containing "STRUCTURE_1z7f", creates the "Structure Box" on the page.
<StructureSection load='1z7f' size='340' side='right'caption='[[1z7f]], [[Resolution|resolution]] 2.10&Aring;' 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'>[[1z7f]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z7F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z7F 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]] 2.1&#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=SR:STRONTIUM+ION'>SR</scene></td></tr>
{{STRUCTURE_1z7f|  PDB=1z7f  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1z7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z7f OCA], [https://pdbe.org/1z7f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z7f RCSB], [https://www.ebi.ac.uk/pdbsum/1z7f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z7f ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribose 2'-amine substitutions are broadly useful as structural probes in nucleic acids. In addition, structure-selective chemical reaction at 2'-amine groups is a robust technology for interrogating local nucleotide flexibility and conformational changes in RNA and DNA. We analyzed crystal structures for several RNA duplexes containing 2'-amino cytidine (C(N)) residues that form either C(N)-G base pairs or C(N)-A mismatches. The 2'-amine substitution is readily accommodated in an A-form RNA helix and thus differs from the C2'-endo conformation observed for free nucleosides. The 2'-amide product structure was visualized directly by acylating a C(N)-A mismatch in intact crystals and is also compatible with A-form geometry. To visualize conformations able to facilitate formation of the amide-forming transition state, in which the amine nucleophile carries a positive partial charge, we analyzed crystals of the C(N)-A duplex at pH 5, where the 2'-amine is protonated. The protonated amine moves to form a strong electrostatic interaction with the 3'-phosphodiester. Taken together with solution-phase experiments, 2'-amine acylation is likely facilitated by either of two transition states, both involving precise positioning of the adjacent 3'-phosphodiester group.


===Crystal structure of 16 base pair RNA duplex containing a C-A mismatch===
Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA.,Gherghe CM, Krahn JM, Weeks KM J Am Chem Soc. 2005 Oct 5;127(39):13622-8. PMID:16190727<ref>PMID:16190727</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_16190727}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1z7f" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 16190727 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_16190727}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z7F OCA].
[[Category: Gherghe CM]]
 
[[Category: Krahn JM]]
==Reference==
[[Category: Weeks KM]]
Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA., Gherghe CM, Krahn JM, Weeks KM, J Am Chem Soc. 2005 Oct 5;127(39):13622-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16190727 16190727]
[[Category: Gherghe, C M.]]
[[Category: Krahn, J M.]]
[[Category: Weeks, K M.]]
[[Category: Duplex]]
[[Category: Mismatch]]
[[Category: Rna]]
 
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