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1z7f

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[[Image:1z7f.gif|left|200px]]<br /><applet load="1z7f" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1z7f.gif|left|200px]]
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caption="1z7f, resolution 2.10&Aring;" />
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'''Crystal structure of 16 base pair RNA duplex containing a C-A mismatch'''<br />
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{{Structure
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|PDB= 1z7f |SIZE=350|CAPTION= <scene name='initialview01'>1z7f</scene>, resolution 2.10&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=SR:STRONTIUM ION'>SR</scene>
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|ACTIVITY=
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|GENE=
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}}
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'''Crystal structure of 16 base pair RNA duplex containing a C-A mismatch'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1Z7F is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=SR:'>SR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z7F OCA].
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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].
==Reference==
==Reference==
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=16190727 16190727]
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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: Protein complex]]
[[Category: Gherghe, C M.]]
[[Category: Gherghe, C M.]]
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[[Category: rna]]
[[Category: rna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:12:49 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:32:07 2008''

Revision as of 13:32, 20 March 2008

Image:1z7f.gif


PDB ID 1z7f

Drag the structure with the mouse to rotate
, resolution 2.10Å
Ligands:
Coordinates: save as pdb, mmCIF, xml



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

1Z7F is a Protein complex structure of sequences from [1]. 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 Thu Mar 20 15:32:07 2008

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