A stereo figure of the 2mFo − DFc electron-density map for the refined model covering the active site. Electron density is shown at a level of 1σ. The zinc ion is shown as a grey sphere and water molecules are shown as red spheres. The acetate ion coordinating the zinc ion is clearly visible in the density map and is found to hydrogen-bond to the conserved His55. The conserved LTXDDG motif of the NodB domain includes Asp114 and Asp115.