Simulated annealing omit electron density maps of BPPS complexes contoured at 4σ; all inhibitor atoms and Mg2+ ions were omitted from structure factor calculations. Carbon, black (ligand) or gray (protein); oxygen, red; nitrogen, blue; phosphorus, magenta; Mg2+ ions, green; water molecules, orange. Metal coordination interactions are indicated by solid black lines and hydrogen bond interactions are indicated by dashed black lines. (A) Inorganic pyrophosphate (PPi). In addition to interactions described in the text, E429 from helix F accepts hydrogen bonds from magnesium-bound water molecules. An ordered buffer molecule (bis-Tris) occupies the active site. (B) 3-Aza-2,3-dihydrogeranyl diphosphate (1). Two water molecules, #110 and #111, bind in the active site cavity along with the inhibitor. (C) BPP. Note that water #110 remains trapped in the active site along with the cyclization product.