Nitrogenase reduces atmospheric N₂ using a two-protein system. The small Fe protein binds 2 MgATP, docks onto the large MoFe protein, transfers exactly one electron to the FeMo-cofactor active site, hydrolyzes both ATP to ADP + Pi, and undocks. This cycle must repeat eight times (states E0→E8) before the accumulated electrons and protons can reduce substrate:
N2 + 8 H+ + 8 e- + 16 MgATP + 16 H2O
-> 2 NH3 + H2 + 16 MgADP + 16 Pi
The reaction is obligately wasteful: even at saturating electron flux, one H₂ is released for every N₂ fixed — it cannot be avoided, only diluted by faster turnover. At low electron flux the enzyme falls back to reducing protons alone, releasing H₂ instead of fixing N₂ at all — a real kinetic property of nitrogenase (Lowe–Thorneley scheme; Simpson & Burris 1984). This sim models that as a flux-dependent partition probability:
P(N2 fixed | E8 reached) = flux / (flux + K), K ≈ 0.6
- Electron flux slider — sets how fast Fe protein completes ATP-driven docking cycles; higher flux both speeds turnover and biases the E8 branch toward productive N₂ reduction.
- N₂ partial pressure slider — scales substrate availability; at low N₂, sites default to unproductive H₂ evolution even with electrons ready.
- Expose to O₂ — the Fe protein's [4Fe-4S] cluster is irreversibly destroyed by O₂; active sites in the background field turn gray and stop cycling permanently, exactly like a real anaerobic nitrogenase prep exposed to air.
- The background field is a population of independent catalytic sites (InstancedMesh), each cycling through its own E-state — the color ramp (blue → gold) shows how many of the 8 electrons each site currently holds.