Structural data of CorA Mg2+ channels show that the five Gly-Met-Asn (GMN) motifs at the periplasmic loop of the pentamer structure form a molecular scaffold serving as a selectivity filter. Unfortunately, knowledge about the cation selectivity of Mg2+ channels remains limited. Since Mg2+ in aqueous solution has a strong first hydration shell and apparent second hydration sphere, the coordination structure of Mg2+ in a CorA selectivity filter is expected to be different from that in bulk water. Hence, this study investigated the hydration structure and ligand coordination of Mg2+ in a selectivity filter of CorA using molecular dynamics (MD) simulations. The simulations reveal that the inner-shell structure of Mg2+ in the filter is not significantly different from that in aqueous solution. The major difference is the characteristic structural features of the outer shell. The GMN residues engage indirectly in the interactions with the metal ion as ligands in the second shell of Mg2+. Loss of hydrogen bonds between inner-and outer shell waters observed from Mg2+ in bulk water is mostly compensated by interactions between waters in the first solvation shell and the GMN motif. Some water molecules in the second shell remain in the selectivity filter and become less mobile to support the metal binding. Removal of Mg2+ from the divalent cation sensor sites of the protein had an impact on the structure and metal binding of the filter. From the results, it can be concluded that the GMN motif enhances the affinity of the metal binding site in the CorA selectivity filter by acting as an outer coordination ligand.