We characterize the rate-limiting interaction of the antibiotic enrofloxacin with OmpF, a channel from the outer cell wall of Escherichia coil. Reconstitution of a single OmpF trimer into planar lipid membranes allows measurement of the ion current through the channel. Penetration of antibiotics causes ion current blockages, and their frequency allows a conclusion on the kinetics of channel entry and exit. In contrast to other antibiotics, enrofloxacin is able to block the OmpF channel for several milliseconds, reflecting high affinities comparable to substrate-specific channels such as the maltodextrin-specific maltoporin. Surprisingly, the presence of a divalent ion such as Mg2+ leads to fast flickering with an increase in the rates of association and dissociation. All-atom computer modeling provides the most probable pathway able to identify the relevant rate-limiting interaction during antibiotic permeation. Mg2+ has a high affinity for the aspartic acid at the 113 position (D113) in the center of the OmpF intracellular binding site. Therefore, the presence of Mg2+ reverses the charge and enrofloxacin may cross the constriction region in its favorable orientation with the carboxylic group first.