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Figure 3.
Figure 3. Details of the AMP/phosphate binding site. (a)
Stereo image of the chemical environment of AMP. Residues
directly contacting the nucleotide are shown as stick models.
Water molecules are drawn as orange spheres and hydrogen bonds
are shown as broken blue lines. (b) The superposition of the AMP
(yellow) and orthophosphate-bound (grey) TthDEAD structures
reveals that an isolated phosphate ion (blue) is not a good
mimic for the nucleotide as several hydrogen bonds of AMP (shown
in blue) are lost in the orthophosphate complex due to a
rotation of orthophosphate relative to the AMP α-phosphate. (c)
90° rotation of the view in (b) showing subtle
rearrangements of the P-loop due to the absence of the base and
ribose moieties. The σ[A]-weighted mF[o]-DF[c] omit electron
density map of orthophospate is contoured in black at 3σ.
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