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Figure 6
Comparison of dimeric cryo-EM and monomeric crystallographic NmqNOR structures. (a) In the crystallographic structure (salmon sticks), the Zn2 binding site (grey sphere) interferes with FeB (magenta sphere), as Glu494 is helping to coordinate Zn2 (yellow dashed lines), whilst the native, non-zinc-bound cryo-EM-derived structure (cyan sticks) shows Glu494 to ligate FeB (brown sphere) in a monodentate fashion via the O∊1 atom, as shown by the red dashed line. (b) Alignment of the crystallographic (salmon cartoon) and cryo-EM structures (one protomer of the dimer is shown as a cyan cartoon) shows distortion of TMII in the crystal structure, possibly owing to the absence of a neighbouring molecule. TMX is also heavily perturbed, possibly owing to Zn1 binding [black dashed box, elaborated in (c)]. (c) Zn1 binding causes significant helical movement of TMX, with the cryo-EM TMX shifted inwards, with Glu573, Glu576 and His577 facing towards the putative proton-transfer channel/solvent in the absence of zinc, with His257 facing towards the cytoplasmic end.

IUCrJ
Volume 7| Part 3| May 2020| Pages 404-415
ISSN: 2052-2525
https://doi.org/10.1107/S2052252520003656