439d
From Proteopedia
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5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3', 5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3'
Overview
The structure of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) has been, determined at 1.6 A resolution and refined to a final R factor of 18.3%, (R(free) = 24.1%). The sequence of the RNA fragment resembles domain E of, Thermus flavus 5S rRNA. A previously undescribed wobble-like G.C base-pair, formation is found. Owing to the observed hydrogen-bond network, it is, proposed that the cytosine is protonated at position N3. The unusual, base-pair formation is presumably strained by intermolecular interactions., In this context, crystal packing and particular intermolecular contacts, may have direct influence on the three-dimensional structure. Furthermore, this structure includes two G.U wobble base pairs in tandem conformation, with the purines forming a so-called 'cross-strand G stack'.
About this Structure
439D is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A resolution., Perbandt M, Vallazza M, Lippmann C, Betzel C, Erdmann VA, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):219-24. PMID:11173467
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