The structure of the unique metal-binding protein, metallothionein (MT), consists of two metal-thiolate-clustered binding domains; the β-domain binds up to three divalent metals and the α-domain binds four. The mechanisms through which the metals are bound and arranged into domains, as well as the function of MT in metal ion homeostasis, remains largely unknown. By utilizing electrospray ionization mass spectrometry (ESI MS) to identify each species, and by comparing the data with simulations, MT 1a was found to bind Zn2+ non-cooperatively. Through a competition experiment between MT and its individual domain peptides, MT was proposed to bind Zn2+ using terminal cysteines initially (into five strong binding sites) before formation of the clusters with binding of the sixth and seventh Zn2+ (into two weaker binding sites). The terminally bound Zn5-MT intermediate is thought to be key to metal acquisition (from zinc-chaperones) and donation (to zinc-dependent apo-enzymes) in maintaining intracellular zinc homeostasis.