The zinc ion (Zn2+) and proton (H+) are critical regulators for the glycine receptor chloride channel in physiological and pathological conditions. Both ions bind to the H109 residue at the extracellular agonist binding domain. However, whether the H109 residue affects the conformation of the remote channel pore is not yet known. In this study, we focus on the loss-of-function mutation, H109A, and use the inhibitory potencies of six structurally-diverse channel pore blockers (niflumic acid, picrotoxin, bilobalide, ginkgolide A, ginkgolide B and ginkgolide C) with various molecular volumes to measure the H109A mutation's effect on channel pore conformation. We found that their inhibitory potencies were mostly reduced by the H109A mutation and the extents of reduction were positively correlated with the molecular volumes of the blockers. In addition, we also found that the H109A mutation slowed both the blocking and unblocking rates of the blockers. Taken together, we propose that the H109A mutation might "narrow" the channel pore, although other forms of conformational change cannot be excluded. This further provides an implication that the H109 residue might allosterically control the channel pore conformation, and that Zn2+ or H+ binding to this site might also alter the conformation of the channel pore.