Domain 3 of the cricket paralysis virus intergenic region ires RNA. Chain: a. Fragment: domain 3 RNA. Engineered: yes. Mutation: yes. RNA (5'-r(p Up Ap Ap Gp Ap Ap Ap Up Up Up Ap Cp Cp U)-3'). Chain: b. Fragment: domain 3 RNA.
Source:
Synthetic: yes. Other_details: in vitro transcription. Synthetic: yes
Resolution:
2.80Å
R-factor:
0.242
R-free:
0.276
Authors:
J.S.Kieft,B.L.Golden,D.A.Costantino,E.Chase
Key ref:
J.S.Kieft
et al.
(2010).
Identification and characterization of anion binding sites in RNA.
Rna,
16,
1118-1123.
PubMed id: 20410239
Identification and characterization of anion binding sites in RNA.
J.S.Kieft,
E.Chase,
D.A.Costantino,
B.L.Golden.
ABSTRACT
Although RNA molecules are highly negatively charged, anions have been observed
bound to RNA in crystal structures. It has been proposed that anion binding
sites found within isolated RNAs represent regions of the molecule that could be
involved in intermolecular interactions, indicating potential contact points for
negatively charged amino acids from proteins or phosphate groups from an RNA.
Several types of anion binding sites have been cataloged based on available
structures. However, currently there is no method for unambiguously assigning
anions to crystallographic electron density, and this has precluded more
detailed analysis of RNA-anion interaction motifs and their significance. We
therefore soaked selenate into two different types of RNA crystals and used the
anomalous signal from these anions to identify binding sites in these RNA
molecules unambiguously. Examination of these sites and comparison with other
suspected anion binding sites reveals features of anion binding motifs, and
shows that selenate may be a useful tool for studying RNA-anion interactions.
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