Summary information and primary citation

PDB-id
2gq4; DSSR-derived features in text and JSON formats
Class
RNA
Method
X-ray (1.35 Å)
Summary
Crystal structure of an RNA racemate
Reference
Rypniewski W, Vallazza M, Perbandt M, Klussmann S, Delucas LJ, Betzel C, Erdmann VA (2006): "The first crystal structure of an RNA racemate." Acta Crystallogr.,Sect.D, 62, 659-664. doi: 10.1107/S090744490601359X.
Abstract
The racemate of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) from Thermus flavus 5S rRNA has been crystallized and examined by X-ray crystallography. The space group is P1(_) with approximate unit-cell parameters a = 26.5, b = 38.0, c = 45.4 Angstrom, alpha = 113.1, beta = 100.5, gamma = 93.3 degrees. The structure was solved by molecular replacement. There are four RNA duplexes in the unit cell. The crystal lattice consists of columns of RNA duplexes. The duplexes are stacked end-to-end and are stabilized by intermolecular base-stacking interactions. Within each column the L-duplexes and D-duplexes are stacked alternately. Every other duplex in each stack has two alternative conformations, approximately equally occupied, corresponding to molecules oriented in opposite directions. Neighbouring columns are related by the crystallographic centre of symmetry. The unit cell also contains approximately 250 ordered water molecules and six ordered calcium ions. A glycerol molecule is visible in the minor groove interacting with a guanosine residue.

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