Several toxic effects arise from Al's presence in living systems, one of them being the alteration of the natural role of enzymes and non-enzyme proteins. Al(III) is capable of entering protein active sites that in normal conditions should be occupied by other metals. Even if Mg(II) is an ubiquitous metal in biological systems, the interference of aluminium in magnesium metabolism is not clear yet. In this work, a systematic study of the affinity of Al(III) for different protein binding sites is presented, with special attention on structural parameters, the role of the charge and the presence of different ligands in the protein cavity. The specificity of the binding site for Al(III) against Mg(II) has been studied, and also the thermodynamical propensity of a Mg(II)/Al(III) exchange. Quantum mechanical methods that proved to be reliable in previous works have been used, namely, the density functional theory (DFT) and polarizable continuum model (PCM).