Fig. 4: The Fd binding pocket.

a The Fd binding pocket is mainly formed by NdhI and NdhH. Fd is shown in cartoon, the NDH subunits are shown in surface mode. Subunits close to Fd are colored differently and other subunits are shown in white. b The electrostatic surface representation of Fd binding pocket. Red represents negative charge, and blue represents positive charge. Fd is shown as yellow cartoon. The positively-charged regions surrounding Fd are highlighted with black dashed circle and labeled. c The interactions between Fd and NdhI/NdhH subunits. The Fe–S clusters and the residues involved in the interactions between Fd and NdhI/NdhH are depicted as sticks and labeled. The hydrogen bonds are shown as black dashed lines. The distance between Fe–S clusters of NdhI and Fd (red dashed line) is indicated. d Fd and NdhV almost symmetrically bind the hairpin loop of NdhI from the opposite sides. The zoom-in view of the region circled by the black dashed line is shown in (e). e Superposition of NDH-Fd and NDH-PQ structures showing the different conformation of the hairpin loop in NdhI subunit. Two positively-charged Lys residues from the hairpin loop of NdhI are hydrogen bonded with residues from Fd. Residues involved in the interactions are shown as sticks and labeled. f The loop regions in NdhN and NdhS (pointed with black arrows) interact with NdhI and/or NdhH and help to stabilize the Fd binding pocket.