Extended Data Fig. 4: Exemplary electron density maps of NosD.

a, The maps section shows a stereo representation of the electron density map around the HMM motif of NosD as indicated in the cartoon of the complex. In the ATP-bound state of the NosF(E154Q) variant complex, the HMM motif (residues H297, M209, M231) are metal-free. b, Electron density map for the NosDFYL complex in GDN micelles, showing the same region as in (a). Zn²⁺ binds to NosL and Cu⁺ is coordinated by the HMM motif of NosD. c, As the NosZDFY complex was formed with the NosF(E154Q) variant that produces a NosDFY complex that cannot receive Cu from NosL, the metal sites of the apo enzyme are vacant. Electron density map at the Cu_A site of N₂OR. The structure of the holo form of the enzyme (right) underlines the absence of the two Cu ions. d, Electron density map at the Cu_Z site in the hub of the β-propeller domain of N₂OR. The Cu-replete protein in the same orientation (right) denotes where the tetranuclear cluster should be located. All maps are normalized and contoured at the 5σ level.