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Figure 2.
Figure 2. Determinants of ATP and RNA Binding
Interacting residues from the N-terminal, middle, and C-terminal
domains are colored yellow, green, and cyan, respectively.
Residues within cloud-shaped bubbles on either side of the bases
indicate hydrophobic/van der Waals interactions. Water molecules
(circles) are color coded based on the degree to which they are
buried within the interior of the protein; those colored dark
blue are completely buried (see Experimental Procedures). Those
colored gray-blue are at the protein surface. Others are colored
intermediate shades of blue depending on how many shells of
water needed to be removed in order for the water atoms to
become exposed. Asp154 and the second Mg^2+ ion are shown in
gray. Eight additional water molecules interact with the
triphosphate moiety of the ATP. These are not shown for clarity,
and because the water structure in this region may be altered
due to the D154A mutation. The base at position −5 interacts
with a neighboring PAP molecule and is not shown.
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