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Figure 4.
Figure 4. (a) The GDP binding site of EF-Tum (molecule A). The Mg
2+
and its six ligands (thin red lines). Besides
the four water molecules coordinating the Mg
2+
, 12 additional water molecules are shown. The waters are roughly
organized in two clusters, one around the Mg
2+
and the phosphate groups, and the other around the ribose ring of
the GDP. (b) The Mg
2+
binding site with selected distances shorter than 3.1 Å . The six Mg-ligand distances (red),
others (blue). Interatomic distances between w1-w4 are not shown, but have an average value of 2.96 Å . The water
molecule w8 is displaced slightly away from the typical position due to the presence of Y92-OH. Except for w8, all
other water molecules have at least two possible hydrogen bond donors/acceptors. The water molecules bridge the
different parts of the binding site, e.g. w7 bridges the NH+3 group of K70 with Omc of P128. (c) Binding site for the
ribose and guanine ring of GDP. The guanine ring is inserted between the aliphatic part of K182 and L221. The NH+3
group of K70 forms hydrogen bonds to w9 and w10, and Omc of D67, instead of hydrogen bonding to the endocyclic
O of the ribose. As for the Mg
2+
-binding site, the well ordered water molecules connect separated parts of the
binding site. The water molecules w9, w10, w11 and w13 connect D155, K182, the ribose ring of GDP and T72.
(d) The environment of the NKXD sequence with helix D (right) and the loop connecting helices E -F (top).
Compared to EF-Tue (yellow), EF-Tum (gray) contains two extra residues, while EF-Tut contains eight extra residues.
The loop connecting helices D-E in EF-Tue and EF-Tut contains an arginine residue, forming a saltbridge to helix D,
R172e-E150e, which is absent in EF-Tum.
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