Members of the pentameric ligand-gated ion channel superfamily (pLGICs) select for a variety of different agonists. Recent structural and mutational analysis has highlighted the relatively conserved role of a box of aromatic residues in coordinating the agonist positive charge. From early modelling based on an acetylcholine-binding protein (AChBP), we proposed that a glutamate residue, conserved in inhibitory GABAA and glycine receptors (GlyR), would replace one aromatic box residue and form a salt-bridge with the primary amine of GABA or glycine agonists. Thus "pinning" the agonist between this Glu and a previously identified arginine from the opposing subunit that interacts with the agonist carboxyl. This proposal has been supported by mutational analysis of GlyRs and structural analysis of a bacterial homolog, ELIC. Here we show that this Glu is a key determinant of agonist selectivity in GABAARs but, surprisingly and in contrast to the GlyR, replacement with the smaller Asp shifts selectivity towards smaller agonists. Seeking an explanation for this apparent contradiction, we show that a series of charged residues provide salt-bridges that constrain the key Glu and determine selectivity for different sized agonists. We show further that an intersubunit hydrogen-bond provides an additional determinant of agonist-size selectivity between GABAARs and GlyRs. Thus, whilst confirming the functional role of this Glu in GABAARs, we have identified two mechanisms that determine agonist-size selectivity between GABAARs and GlyRs, despite using the same two charged coordinating residues. Firstly, salt-bridges constrain the side-chain of the Glu and secondly, a hydrogen-bond alters the distance between these two coordinating residues.