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. Author manuscript; available in PMC: 2015 Oct 20.
Published in final edited form as: Nat Commun. 2015 Apr 20;6:6874. doi: 10.1038/ncomms7874

Fig. 2.

Fig. 2

Inner and outer cores of YdaH. (a) The inner core of YdaH, comprising TMs 1, 2, 5, 6 and 7 (colored slate), contributes to dimerization as well as formation of a frame-like structure housing the outer core of the protomer. The outer core of YdaH is composed of TMs 3, 4, 8, 9 as well as HPs 1 and 2 (colored yellow). (b) The outer core of YdaH forms a channel (colored purple) spanning approximately from the middle of the inner membrane up to the periplasmic space. This channel was calculated using the program CAVER (http://loschmidt.chemi.muni.cz/caver). The secondary structural elements of the YdaH protomer are in yellow. Residues D180, N390, W400, P418, R426, D429 and N433 are in green sticks. The bound sodium ion is shown as an orange sphere. (c) The bound Na+ (orange sphere) is found to coordinate with N390, G394, D429, N433 and a water molecule (red sphere). The Fo-Fc map, showing the bound Na+ and H2O, is contoured at 3.0 σ (blue mesh).