Metallothioneins (MTs) are metal-binding proteins with low molecular weight and conservative cysteine residues. Metallothionein-4 (MT-4), one of MT isoforms, is first reported to be distributed in a tissue-specific manner, mainly in stratified squamous epithelia. Here, we compare the properties of metal-thiolate clusters in MT-4 to those in MT-1 and MT-3, including the stabilities toward both pH change and EDTA, as well as the exposure of thiolates to solvent. The metal-thiolate clusters in MT-3 show different property and activity to the reactions compared with MT-4 and MT-1. The structure of metal-thiolate clusters in MT-4 is similar to that of MT-1 from the UV and CD spectra. During pH titration and DTNB reaction, MT-4 and MT-1 exhibit comparable behavior. But while reacting with EDTA, the metal-thiolate clusters in MT-4 are more stable than those of MT-1. We suppose the negative charge of the beta-domain of MT-4 prevents the EDTA attack to MT-4.