2et4
From Proteopedia
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Complex Between Neomycin B and the 16S-RRNA A-Site
Overview
The crystal structures of six complexes between aminoglycoside antibiotics, (neamine, gentamicin C1A, kanamycin A, ribostamycin, lividomycin A and, neomycin B) and oligonucleotides containing the decoding A site of, bacterial ribosomes are reported at resolutions between 2.2 and 3.0 A., Although the number of contacts between the RNA and the aminoglycosides, varies between 20 and 31, up to eight direct hydrogen bonds between rings, I and II of the neamine moiety are conserved in the observed complexes., The puckered sugar ring I is inserted into the A site helix by stacking, against G1491 and forms a pseudo base pair with two H-bonds to the, Watson-Crick sites of the universally conserved A1408. This central, interaction helps to maintain A1492 and A1493 in a bulged-out, conformation. All these structures of the minimal A site RNA complexed to, various aminoglycosides display crystal packings with intermolecular, contacts between the bulging A1492 and A1493 and the shallow/minor groove, of Watson-Crick pairs in a neighbouring helix. In one crystal, one empty A, site is observed. In two crystals, two aminoglycosides are bound to the, same A site with one bound specifically and the other bound in various, ways in the deep/major groove at the edge of the A sites.
About this Structure
2ET4 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding., Francois B, Russell RJ, Murray JB, Aboul-ela F, Masquida B, Vicens Q, Westhof E, Nucleic Acids Res. 2005 Oct 7;33(17):5677-90. Print 2005. PMID:16214802
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