Iron-sulfur clusters in Azotobacter ferredoxin at 2.5 A resolution

X-ray crystallographic study of the ferredoxin-like protein (iron-sulfur protein III) from Azotobacter vinelandii has been extended to 2.5-A resolution. A 4.0-A resolution electron density map revealed that the molecule contains two Fe-S clusters of differing size and shape separated by 12 A (Stout, C.D. (1979) Nature 279, 83-84). Recent Mössbauer results by Emptage et al. (Emptage, M.H., Kent, T.A., Huynh, B.H., Rawlings, J., Orme-Johnson, W.H., and Münck, E. (1980) J. Biol. Chem. 255, 1793-1796) have shown that the molecule contains 7 iron atoms as a high potential iron protein-like Fe4 center and a novel 3-Fe center. The 2.5-A electron density map shows two distinctly different Fe-S clusters. The larger cluster consists of a tetranuclear [4Fe-4S] core ligated to the protein at each iron atom. The smaller cluster is distinctly planar and cannot be modeled with [2Fe-2S] or [4Fe-4S] structures. The best model for this cluster is a [3Fe-3S] core. The protein makes six contacts with this cluster.