4P20: Crystal structures of the bacterial ribosomal decoding site complexed with amikacin

Citation:
Abstract
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.
PDB ID: 4P20Download
MMDB ID: 119619
PDB Deposition Date: 2014/2/28
Updated in MMDB: 2017/12
Experimental Method:
x-ray diffraction
Resolution: 2.7  Å
Source Organism:
Biological Unit for 4P20: dimeric; determined by software (PISA)
Molecular Components in 4P20
Label Count Molecule
Nucleotide(1 molecule)
2
5'-r(*up*up*gp*cp*gp*up*cp*ap*cp*ap*cp*cp*gp*gp*up*gp*ap*ap*gp*up*cp*gp*c)-3'
Molecule annotation
Chemicals (2 molecules)
1
2
* Click molecule labels to explore molecular sequence information.

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