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Figure 1.
The crystal structure of
Å resolution depicted in (A) cartoon form and (B) as a molecular surface in the same
orientation. The structure is shown from the beginning of ß-strand 1 to the end of
{alpha} -helix 3, since the regions outside these bounds were random coil or not
visible in the density. The GXXG motif, common to this oligonucleotide-binding motif, is
coloured blue. The `variable loop' region between ß-sheets 2 and 3 is coloured pink. These
regions bound the hydrophobic oligonucleotide-binding cleft that accommodates C-rich RNA
or ssDNA. (C) The electrostatic potential emanating from the {alpha} CP1-KH3
structure calculated using the APBS software package (http://agave.wustl.edu/apbs/)
(39-43). Potential contours are shown at +1 kT/e (blue) and -1 kT/e (red) and
obtained by solution of the linearized Poisson-Boltzmann equation at 150 mM ionic strength
with a solute dielectric of 2 and a solvent dielectric of 78.5. The blue contour
represents a striking positive potential directing oligonucleotides to the binding cleft.
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