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[[Image:1yzd.gif|left|200px]]


{{Structure
==Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair==
|PDB= 1yzd |SIZE=350|CAPTION= <scene name='initialview01'>1yzd</scene>, resolution 2.35&Aring;
<StructureSection load='1yzd' size='340' side='right'caption='[[1yzd]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
|SITE=
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene>
<table><tr><td colspan='2'>[[1yzd]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YZD FirstGlance]. <br>
|ACTIVITY=
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5M:2-AMINE-CYTIDINE-5-MONOPHOSPHATE'>A5M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1yzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yzd OCA], [https://pdbe.org/1yzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yzd RCSB], [https://www.ebi.ac.uk/pdbsum/1yzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yzd ProSAT]</span></td></tr>
 
</table>
'''Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Gherghe CM]]
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.
[[Category: Krahn JM]]
 
[[Category: Weeks KM]]
==About this Structure==
1YZD is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YZD OCA].  
 
==Reference==
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: Protein complex]]
[[Category: Gherghe, C M.]]
[[Category: Krahn, J M.]]
[[Category: Weeks, K M.]]
[[Category: CA]]
[[Category: 2'-amine]]
[[Category: duplex]]
[[Category: rna]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:29:23 2008''

Latest revision as of 09:01, 14 February 2024

Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair

1yzd, resolution 2.35Å

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