1 SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056 Basel, Switzerland; Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
2 Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke Street West, Montréal, QC H4B 1R6, Canada.
3 Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke Street West, Montréal, QC H4B 1R6, Canada. Electronic address: guillaume.lamoureux@concordia.ca.
4 SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056 Basel, Switzerland; Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland. Electronic address: simon.berneche@isb-sib.ch.

In human cells, membrane proteins of the rhesus (Rh) family excrete ammonium and play a role in pH regulation. Based on high-resolution structures, Rh proteins are generally understood to act as NH3 channels. Given that cell membranes are permeable to gases like NH3, the role of such proteins remains a paradox. Using molecular and quantum mechanical calculations, we show that a crystallographically identified site in the RhCG pore actually recruits NH4(+), which is found in higher concentration...