The first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D–NaI complex

ArticleinActa Crystallographica Section D Biological Crystallography · May 2010with3 Reads
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    Abstract

    The crystal structure of the nonstoichiometric complex of
    gramicidin D with NaI has been studied using synchrotron
    radiation at 100 K. The limiting resolution was 1.25 A ° and the
    R factor was 16% for 19 883 observed reflections. The general
    architecture of the antiparallel two-stranded gramicidin
    dimers in the studied crystal was a right-handed antiparallel
    double-stranded form that closely resembles the structures of
    other right-handed species published to date. However, there
    were several surprising observations. In addition to the
    significantly different composition of linear gramicidins
    identified in the crystal structure, including the absence of
    the gramicidin C form, only two cationic sites were found in
    each of the two independent dimers (channels), which were
    partially occupied by sodium, compared with the seven sites
    found in the RbCl complex of gramicidin. The sum of the
    partial occupancies of Na+ was only 1.26 per two dimers and
    was confirmed by the similar content of iodine ions (1.21 ions
    distributed over seven sites), which was easily visible from
    their anomalous signal. Another surprising observation was
    the significant asymmetry of the distributions and occupancies
    of cations in the gramicidin dimers, which was in contrast
    to those observed in the high-resolution structures of the
    complexes of heavier