The outer membrane (OM) of Gram-negative bacteria is a unique asymmetric lipid bilayer containing lipopolysaccharides (LPS) in the outer leaflet and phospholipids in the inner leaflet. Due to the lack of porins with large pores, the substrate-specific outer membrane proteins play a crucial role in the uptake of small molecules in Pseudomonas aeruginosa. In this study, we report the influences of OM compositions on the ion permeation properties of OccK5 (also known as OpdH), such as ion selectivity and diffusion constants, using all-atom molecular dynamics simulations. The simulations indicate that OccK5 shows a remarkable anion selectivity independent of the OM composition and effective cation concentration. Intriguingly, the outer core and O-antigens of LPS sterically occlude the channel entrance and decrease the diffusion constants of ions approaching the channel, which was also observed in our previous OmpF porin simulations in Escherichia coli OMs. Our results emphasize the role of native membranes in fine-tuning the functional properties of membrane channels.