4p20: Difference between revisions
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''' | ==Crystal structures of the bacterial ribosomal decoding site complexed with amikacin== | ||
<StructureSection load='4p20' size='340' side='right' caption='[[4p20]], [[Resolution|resolution]] 2.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4p20]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g5q 2g5q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P20 OCA]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKN:(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide'>AKN</scene><br> | |||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4p20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p20 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4p20 RCSB], [http://www.ebi.ac.uk/pdbsum/4p20 PDBsum]</span></td></tr> | |||
<table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Amikacin is the 4,6-linked aminoglycoside modified at position N1 of the 2-deoxystreptamine ring (ring II) by the L-haba group. In the present study, the crystal structure of a complex between oligonucleotide containing the bacterial ribosomal A site and amikacin has been solved at 2.7 A resolution. Amikacin specifically binds to the A site in practically the same way as its parent compound kanamycin. In addition, the L-haba group interacts with the upper side of the A site through two direct contacts, O2*...H-N4(C1496) and N4*-H...O6(G1497). The present crystal structure shows how the introduction of the L-haba group on ring II of aminoglycoside is an effective mutation for obtaining a higher affinity to the bacterial A site. | |||
Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group.,Kondo J, Francois B, Russell RJ, Murray JB, Westhof E Biochimie. 2006 Aug;88(8):1027-31. Epub 2006 Jun 13. PMID:16806634<ref>PMID:16806634</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Francois, B.]] | |||
[[Category: Kondo, J.]] | |||
[[Category: Murray, J B.]] | |||
[[Category: Russell, R J.M.]] | |||
[[Category: Westhof, E.]] | |||
[[Category: Amikacin]] | |||
[[Category: Aminoglycoside]] | |||
[[Category: Haba group]] | |||
[[Category: Ribosomal decoding site]] | |||
[[Category: Rna]] | |||
[[Category: X-ray analysis]] | |||
Revision as of 08:10, 7 May 2014
Crystal structures of the bacterial ribosomal decoding site complexed with amikacin
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