439D

5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3', 5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3'

Summary for 439D

• Entry DOI: 10.2210/pdb439d/pdb
• Descriptor: RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3'), RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3'), BARIUM ION, ... (4 entities in total)
• Functional Keywords: fragment of 5s rrna, a-rna, rna
• Total number of polymer chains: 2
• Total formula weight: 5252.48

Authors

Perbandt, M.,Lorenz, S.,Vallazza, M.,Erdmann, V.A.,Betzel, C. (deposition date: 1999-01-05, release date: 2001-09-14, Last modification date: 2023-12-27)

Primary citation

Perbandt, M.,Vallazza, M.,Lippmann, C.,Betzel, C.,Erdmann, V.A.
Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A resolution.
Acta Crystallogr.,Sect.D, 57:219-224, 2001

PubMed Abstract: 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'.

PubMed: 11173467
DOI: 10.1107/S0907444900017042

Experimental method

X-RAY DIFFRACTION (1.6 Å)