1z7f
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1z7f |SIZE=350|CAPTION= <scene name='initialview01'>1z7f</scene>, resolution 2.10Å | |PDB= 1z7f |SIZE=350|CAPTION= <scene name='initialview01'>1z7f</scene>, resolution 2.10Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=SR:STRONTIUM ION'>SR</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1z7f|1Z7F]], [[1yrm|1YRM]], [[1yy0|1YY0]], [[1yzd|1YZD]] | ||
| + | |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> | ||
}} | }} | ||
| Line 24: | Line 27: | ||
[[Category: Krahn, J M.]] | [[Category: Krahn, J M.]] | ||
[[Category: Weeks, K M.]] | [[Category: Weeks, K M.]] | ||
| - | [[Category: SR]] | ||
[[Category: duplex]] | [[Category: duplex]] | ||
[[Category: mismatch]] | [[Category: mismatch]] | ||
[[Category: rna]] | [[Category: rna]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:30:55 2008'' |
Revision as of 22:30, 30 March 2008
| |||||||
| , resolution 2.10Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Related: | 1Z7F, 1YRM, 1YY0, 1YZD
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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 Mon Mar 31 01:30:55 2008
Categories: Protein complex | Gherghe, C M. | Krahn, J M. | Weeks, K M. | Duplex | Mismatch | Rna
