Ryanodine receptors (RyRs) are the largest known ion channels, and are of central importance for the release of Ca2+ from the sarco/endoplasmic reticulum (SR/ER) in a variety of cells. In cardiac and skeletal muscle cells, contraction is triggered by the release of Ca2+ into the cytoplasm and thus depends crucially on correct RyR function. In this work, in silico mutants of the RyR pore were generated and MD simulations were conducted to examine the impact of the mutations on the Ca2+ distribution. The Ca2+ distribution pattern on the luminal side of the RyR was most affected by G4898R, D4899Q, E4900Q, R4913E, and D4917A mutations. MD simulations with our wild-type model and various ion species showed a preference for Ca2+ over other cations at the luminal pore entrance. This Ca2+-accumulating characteristic of the luminal RyR side may be essential to the conductance properties of the channel.