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Figure 5.
Figure 5 Docking approach for the complex between Gyp1p and
Ypt51p-GTP, modelled manually on the basis of known GAP–GTPase
structures. (A) Active site of the complex formed between
p120-GAP and H-Ras p21(GDP-AlF[3]). The hydrogen bonds between
GAP residues Arg789 and Arg903 and H-Ras p21 residues Gln61 and
Glu63 as well as with AlF[3] are indicated. This specific
hydrogen bond network and the orientation of the side chains
were used as a model for manual docking of Ypt51-GTP to
Gyp1-46p. (B) Close-up view of the active site in the putative
Gyp1-46p–Ypt51-GTP complex. For the interaction between the
side chain of Arg343 and the  -phosphate
group, the salt bridge formed between Arg343 and Asp340 has to
be broken. Gln66 of Ypt51p is well oriented to become positioned
closer to the -phosphate
by forming a hydrogen bond between its side chain and the main
chain carbonyl group of Arg343 of Gyp1p. (C) Ribbon
representation of the putative complex. The orientation of
Gyp1-46p is the same as in Figure 1. The essential arginine
Arg343 of Gyp1p, the active site glutamine Gln66 of Ypt51p and
the bound nucleotide GTP are shown in ball-and-stick
representation. This figure was generated using the programs
BOBSCRIPT (Esnouf, 1997) and raster3D (Merritt and Murphy, 1994).
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