The ground and excited state properties and ligand-binding capabilities of [ZnFe3S4](2+,+), [CoFe3S4](2+,+), and [MnFe3S4](+) clusters in Pyrococcus furiosus Fd have been investigated by the combination of EPR, variable-temperature magnetic circular dichroism (VTMCD), and MCD magnetization studies. The ground state spins, S = 5/2 for [ZnFe3S4](+), S = 2 for [ZnFe3S4](2+), S = 1 for [CoFe3S4](+), S = 1/2 for [CoFe3S4](2+), and S = 0 for [MnFe3S4](+), are consistent with a simple coupling scheme involving antiparallel interaction between the high-spin divalent metal ion and an S = 5/2 [Fe3S4](+) or S = 2 [Fe3S4](0) cluster fragment. Redox potentials (vs NHE) were determined by dye-mediated EPR titrations at pH 7.6, E(m) -241 +/- 20 mV for [ZnFe3S4](2+,+) E(m) = -163 +/- 10 mV for [CoFe3S4](2+,+), and E(m) > -100 mV for [MnFe3S4](2+,+), indicating that the potentials for [MFe(3)S(4)](2+,+) clusters in P. furiosus Fd are ordered M = Fe < Zn < Co < Mn or Ni. On the basis of changes in EPR and/or VTMCD spectra, evidence is presented for cyanide binding at the unique metal site of the [ZnFe3S4](+) and [CoFe3S4](+) clusters and for 2-mercaptoethanol binding at the Zn site of the [ZnFe3S4](+) cluster. The ground and excited state properties of the thiolate-bound [ZnFe3S4](+) cluster in P. furiosus Fd are very similar to those of the equivalent cluster in Desulfovibrio gigas FdII, indicating coordination of the Zn by the indigenous cysteinate in this protein. The site specific reactivity, intracluster magnetic interactions, and redox properties of heteronuclear cubanes in general are discussed in light of these results.