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Figure 1.
Figure 1 Features of the electron-density maps that reflect
alternate conformations. (a) Before (left) and after (right)
modeling alternate configurations of residues 126-129 in
structure IIA. The 2F[o] - F[c] map contoured at 1  is
shown in light blue, the negative difference map (F[o] - F[c]
contoured at -3 )
shown in red and the positive difference map (contoured at 3
)
shown in bright blue. The same maps are shown at the same
contour levels after the addition of alternates and are
superimposed on the model of residues 126-129 with alternate
conformations (shaded blue). The alternate side-chain positions
are indicated by asterisks. The `backrub' motion of Arg127
(Davis et al., 2006[Davis, I. W., Arendall, W. B. III,
Richardson, D. C. & Richardson, J. S. (2006). Structure, 14,
265-274.]) is indicated by two arrows. A significant translation
of the peptide perpendicular to the viewer is obscured in this
orientation (see Fig. 2-a). (b) A peptide flip between Gln107
and Gly108 of the motif I P-loop in structure IIA. Note the
water hydrogen bonded to the `flipped' configuration of the
Gly108 amide nitrogen. There is an `unexplained' density (likely
to be a buffer molecule) bound within the P-loop (at the
center). (c) Two conformations of the conserved DARGG loop, the
first in structure IA and the second in structure IIA.
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