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This is the X-ray structure of a 7-iron ferredoxin, [3Fe-4S][4Fe-4S], from a bacterium. These proteins have a distinctive red colour due to a sulfur to iron charge transfer transition (LMCT). The [Fe3S4(S-cys)3]-2/-3 cluster serves as an electron carrier.
This is the backbone of the protein. The [4Fe-4S] cluster (labeled) is at the surface of this small protein and could act as a relay to pass electrons to and from the [3Fe-4S] cluster. The Fe4S4 cluster exists in two oxidation levels, an oxidized form [Fe4S4]2+2 (shown here) and a reduced form [Fe4S4]+. The oxidized form is comprised of two Fe(III) and two Fe(II) and the reduced form, of one Fe(III) and three Fe(II). An unusually oxidized [Fe4S4]+3 state is found in the high-potential iron protein (HiPIP) (not shown). In the oxidized state shown here, [Fe4S4]2+2, electrons are delocalized over the cluster so that the average oxidation state of each iron is effectively 2.5.
In the ribbon display beta-sheets are coloured in red and alpha- helices are coloured in blue. The iron ions are bound to the enzyme by cysteine thiolate groups and are bridged by sulfide ligands to form clusters. The sequence -Cys-X7-Cys- (or -Cys-X5-Cys- in other proteins) is characteristic of a [3Fe-4S] cluster. The [3Fe-4S] cluster has the shape of a cube with one vertex missing. This cluster would become a [4Fe-4S] cluster if an Fe3+ were to add to the vacant site in between the three sulfide ligands (labeled) and a Cys were to coordinate. In this protein Cys11 is not in the correct orientation to do this. The redox potential of this center is probably also about -0.3 V.
The Fe4S4 cluster has a cubane-type structure which can be visualized as a dimer of two Fe2S2 units. The sulfido groups in Fe4S4 bridge three iron centers rather than the two in Fe2S2. The Fe-Fe separations are approximately 2.7 Å The redox potential of this center is about -0.3 V. However different Fe4S4 proteins can have potentials ranging from -0.4 V to +0.35 V depending on the accessibility of the three oxidation levels, the protein environment and the types of ligands attached to the Fe center (see the tour of Hydrogenase).
This is the core of the oxidized protein. All the iron ions are in a tetrahedral coordination environment.
This is the core of the reduced protein. The change in Fe-S bond lengths is minimal upon reduction. This makes electron transfer rapid.
This is the structure of the reduced protein. Feel free to play around with it and all the other molecules displayed in the previous pages.