The interactions between the protein α-synuclein and the Zn(II) and Al(III) cations at different sites were studied at the M06/6-311+G(d,p)/SMD and the ωB97X-D/6-311+G(d,p)/SMD levels of theory. For Zn(II), previous experimental studies determined the presence of a high affinity site at Asp121 and a lower affinity one at His50. As for Al(III), an in vitro study showed it to be the most effective cation to induce structural changes in α-synuclein and to accelerate its aggregation. Besides Zn(II) and Al(III), Cu(II) also binds α-synuclein (in fact, its complexes are the most studied and the best characterized ones) forming square planar complexes, and several binding sites are known for it, involving Met1-Asp2 (only in nonacetylated α-synuclein), His50, and Asp121. Herein, we applied a simple theoretical methodology, which satisfactorily reproduces experimental geometries and energies for complexes of N-terminally acetylated α-synuclein with Cu(II), to study Zn(II) and Al(III) complexes at those same sites, as well as at some structurally analogous alternative sites. We found binding geometries for Zn(II) and Al(III) that differ from the ones for Cu(II). These results can help to understand the interactions between α-synuclein and metals, one of the factors leading to the formation of potentially neurotoxic α-synuclein aggregates.