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

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