Figure 2. Active-site architecture.

(A) Stereo image of substrate-free PPAD CD, which actually corresponds to a thiopyridine modified state, with the Michaelis-loop (V²²⁶-V²³⁷) shown in red. Selected side chains are displayed with their carbons in light blue and labeled. (B) Same view as in (A) of the substrate-mimic complex, with the Michaelis-loop in green, unmodified cysteines, side-chain carbons in tan and relevant solvent molecules to illustrate the NH₃-exit/H₂O-entry and hydroxide channels as spheres in light blue (see also Fig. 4a). The bound aspartate-glutamine dipeptide is further shown with its carbons in turquoise. ① labels D¹³⁰ and ② labels D²³⁸. (C) Same view as in (A) and (B) of the substrate complex, with the Michaelis-loop in green, unmodified cysteine C²³⁹ (C³⁵¹ is replaced by alanine), and side-chain carbons in pink. The bound methionine-arginine dipeptide is further depicted with its carbons in purple. ① labels D¹³⁰ and ② labels D²³⁸.