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Figure 3.
FIG. 3. Stereo views of three sodium ions binding sites of
AmyK38 and BLA (Protein Data Bank accession code 1bli [PDB]
(1)). Pentagonal and quadrilateral bipyramidal cages surrounding
metal ions are drawn by solid or broken lines. Sodium and
calcium ions are drawn as yellow and sky-blue spheres,
respectively. These figures were drawn by MOLSCRIPT, Raster3D,
and Conscript (34-36). In a, the  [A] weighted omit map
(lightblue; contoured at 4.0 ) is shown, and refined
models of the Na I site of wild-type AmyK38 are shown in the
upper section. The model in the lower section is the
calcium-sodium-calcium triad containing the Ca I site of BLA
corresponding to the Na I site of AmyK38. In b, the [A]
weighted omit map (light blue; contoured at 4.0 ) is
shown, and refined models of the Na II site of wild-type AmyK38
are shown in the upper section. The model in the lower section
is the Ca III site of BLA corresponding to the Na II site of
AmyK38. In c, the [A] weighted omit map
(light blue; contoured at 4.0 ) is shown, and the
refined model of the Na III site of wild-type AmyK38 is shown in
the upper section. The model in the lower section is the site of
BLA corresponding to the Na III site of AmyK38. d, the
superimposition of the refined structure of N289H AmyK38 on BLA
around the corresponding site of the Na III site in wild-type
AmyK38. The model of BLA is drawn transparently.
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