Fig. 2. Nucleotide-binding pocket in the G-domain of IF2.

a The EM density of the GDP nucleotide and switch 2 (sw2) region in compact IF2 is shown as black and gray mesh, respectively, sw1 as orange mesh and the P-loop as pink mesh. The lack of density for sw1 (orange) indicates that it is disordered. The catalytic His³⁹⁹ residue in sw2 of IF2-GDP is oriented away from GDP and locates 13 Å from the phosphate oxygen of A2649 (E. coli A2662) in the SRL. b In extended IF2, the catalytic His³⁹⁹ is directed toward the γ-phosphate of GDPCP through the hydrophobic gate consisting of residues Val³⁵¹ of the P-loop and Ile³⁷⁵ of sw1. In this position, His³⁹⁹ is positioned to interact with the phosphate oxygen of A2649 (A2662) in the SRL. Residues Thr³⁷⁶ of sw1 and Thr³⁵⁶ of the P-loop, together with the β- and γ-phosphate oxygen atoms of GDPCP, coordinate a magnesium ion (green).