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1z7f

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[[Image:1z7f.gif|left|200px]]
[[Image:1z7f.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 1z7f |SIZE=350|CAPTION= <scene name='initialview01'>1z7f</scene>, resolution 2.10&Aring;
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The line below this paragraph, containing "STRUCTURE_1z7f", creates the "Structure Box" on the page.
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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{{STRUCTURE_1z7f| PDB=1z7f | SCENE= }}
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|RELATEDENTRY=[[1z7f|1Z7F]], [[1yrm|1YRM]], [[1yy0|1YY0]], [[1yzd|1YZD]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1z7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z7f OCA], [http://www.ebi.ac.uk/pdbsum/1z7f PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1z7f RCSB]</span>
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'''Crystal structure of 16 base pair RNA duplex containing a C-A mismatch'''
'''Crystal structure of 16 base pair RNA duplex containing a C-A mismatch'''
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==About this Structure==
==About this Structure==
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1Z7F 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=1Z7F OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z7F OCA].
==Reference==
==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]
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]
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[[Category: Protein complex]]
 
[[Category: Gherghe, C M.]]
[[Category: Gherghe, C M.]]
[[Category: Krahn, J M.]]
[[Category: Krahn, J M.]]
[[Category: Weeks, K M.]]
[[Category: Weeks, K M.]]
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[[Category: duplex]]
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[[Category: Duplex]]
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[[Category: mismatch]]
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[[Category: Mismatch]]
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[[Category: rna]]
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[[Category: Rna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 17:16:22 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:30:55 2008''
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Revision as of 14:16, 3 May 2008

Image:1z7f.gif

Template:STRUCTURE 1z7f

Crystal structure of 16 base pair RNA duplex containing a C-A mismatch


Overview

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.

About this Structure

Full crystallographic information is available from 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:16190727 Page seeded by OCA on Sat May 3 17:16:22 2008

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