Fig. 2.

Binding of 3-NOP to methyl-coenzyme M reductase (MCR) as suggested by molecular docking. The crystal structure of inactive isoenzyme I from M. marburgensis was used in the docking experiments (25). (A) MCR-catalyzed reaction. CH₃-S-CoM, methyl-coenzyme M; CoM-S-S-CoB, heterodisulfide of coenzyme M and coenzyme B; HS-CoB, coenzyme B. (B) 3-NOP in the active site with its nitrate group in electron transfer distance to Ni(I) of F₄₃₀ and its hydroxyl group interacting via a water molecule with Arg120. (C) 3-NOP in the active site with its hydroxyl group in coordination distance to Ni(I) of F₄₃₀ and its nitrate group interacting with Arg120. (D) Methyl-coenzyme M (CH₃-S-CoM) in the active site with its thioether sulfur in electron transfer distance to Ni(I) and its sulfonate group interacting with both a water molecule and Arg120. The molecules 3-NOP, CH₃-S-CoM, and coenzyme B (HS-CoB) are drawn as ball-and-stick models in orange and F₄₃₀ in light gray highlighting nitrogen in blue, oxygen in red, sulfur in yellow, and nickel(I) as a green sphere. The position of methyl-coenzyme M obtained via docking is almost identical to that found via EPR measurements of active MCR (28).