The crystal structures of C. thermophilum Vps1 GG in complex with GMPPCP, GDP.AlF₄⁻, and GDP. (A–C) The structure of Vps1 GG_GMPPCP. GMPPCP is shown in stick representation, and the Mg²⁺ is shown in green. Ordered waters are shown in red. (D–F) The structure of Vps1 GG_GDP.AlF4-. GDP and AlF₄⁻ are shown as stick representations. Mg²⁺ and Na⁺ are shown as green and purple spheres, respectively. (G–I) The structure of Vps1 GG_GDP. A crystallographic twofold axis is shown as a gray arrow. No ordered density for BSE was observed. Coloring as in A. (B, E, and H) Nucleotide binding pockets for Vps1 GG_GMPPCP, GG_GDP.AlF4-, and GG_GDP shown in A, D, and G with the molecular surface overlaid and shown transparently in gray. (C, F, and I) Details of the nucleotide-binding pockets of the structures shown in A, D, and G. (J) 2F_obs-F_calc maps (contoured at 1 σ) of the nucleotide, nucleotide analogue, or transition state analog of each structure.