358
T. Miyakawa et al.
Fig. 19.7 The angular distribution of used for angular distribution of water molecules in the shell
with radius from 3.5 Å to 4.0 Å around PG in Hras-GTP (a) and around PB in Hras-GDP (b)
Fig. 19.8 The direction angle of water molecules averaged over the volume element such
that r 0 < r < r 1 , θ 0 < θ < θ 0 + Δθ, φ 0 < φ < φ 0 + Δφ, where r 0 = 3.5 Å, r 1 = 4.0 Å, and
Δθ = Δφ = 9 ◦
rection angle > 50 ◦ as shown by the simple contour of 50 ◦ in Fig. 19.8(b). The
direction of water molecules is related to the capability of water molecules sitting
on the space restricted by the atoms in the phosphate of guanine nucleotide. This difference of direction angle between in Hras-GTP and in Hras-GDP possibly causes
the difference of density at the area θ ∼ 30 ◦ , φ ∼ 0 ◦ . In future work, in order to confirm the relation between the direction of water molecules and the density of water
molecules, we need to investigate the restrictions on water molecules around PG in
GTP and PB in GDP by the amino acid residues, Mg 2+ , and crystallization water.
And we need to investigate the possible directions of water molecules around PG in
GTP and around PB in GDP.
19.4 Summary
Differences of structures between Hras-GTP and Hras-GDP are presented in
switch I and II regions. The value of the first hydration radii defined from the RDF
of water molecules with respect to phosphorus atoms in GTP and GDP is from 4.63
to 4.88 Å. Averaged number of water molecules in the first hydration sphere with