2gpm | pdb_00002gpm

Crystal structure of an RNA racemate

spinqualitylabelsall models 2gpm, resolution 1.40Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2gpm is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA NonStd Res: 0C, 0G, 0U Related: 2g32, 2gq4, 2gq5, 2gq6, 2gq7 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum Publication Abstract from PubMed 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. The first crystal structure of an RNA racemate.,Rypniewski W, Vallazza M, Perbandt M, Klussmann S, Delucas LJ, Betzel C, Erdmann VA Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):659-64. Epub 2006, May 12. PMID:16699193 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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