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= Rubredoxin =

Electron Transfer Rate
The electron self-exchange rate is most accurately determined by nuclear magnetic resonance linewidths since the Fe 2+ ions give paramagnetic peak broadening while the Fe+ ion is diamagnetic and therefore causes no broadening.

The electron transfer rate has three parameters it depends on electronic coupling, reorganization energy and free energy of reaction (ΔG°)

Protein mechanism and effects
The amide NH---S-Cys H-bonding lowers the inner sphere reorganization energy giving more rapid electron transfer and the Leu gate stabilizes the Fe 2+ reduced form shifts the redox potential to more postive E0 values. The protein mechanism for the electron transfer of rubredoxin occurs in two steps. The first protein effect, is through the expansion of iron-sulfur bond lengths upon reduction and the shortening of hydrogen bond lengths ensure a better electrostatic stabilization of the negative charge. The other protein effect, is gating mechanism which is created from the conformational changes of Leucine 41. The leucine 41 has a non-polar side chain that allows for transient penetration of the water molecules. This increases the polarity of the of the redox site environment. The Leu41 side chain has two different conformations; reduced and the oxidized form. The conformation in the reduced form is open and allows water molecules near the [Fe(S-Cys)4] 2+ active site and stabilizing the higher net positive charge of the reduced Fe 2+ oxidation state. This shifts the potential 50 mV more positive as indicated by Leu41 – Ala site -directed mutagenesis shift the Fe 3+/2+ redox potential 50 mV more positive. The confirmation allows for the infiltration of water molecules which lets the formation of the strongly H-bonded to attach.

Fe-S bonding
The iron site found in rubredoxins contains a single iron bound by four thiolates from cysteine residues in tetrahedral geometry. Evidence suggests that the thiolate – iron bond is highly covalent and therefore contributes to redox properties on the site. Before reduction, the electron density is strongly delocalized onto the ligands. The reduction in covalency leads to a higher effective nuclear charge on the Iron ion. Rubredoxin has a high covalency and also a low reduction potential. X-ray absorption spectroscopy shows ligand field transitions and the change in hydrogen bonding in the protein. The reduction potentials of various rubredoxin proteins range from -60 to +5 mV. The difference comes from dielectric medium, charge interactions in the area of site and hydrogen bonding

Isolation
There have been a few different rubredoxin proteins identified. It is Isolated from ferredoxin observed in extracts of Clostridium pasteurianum. The protein can be a substitute for ferredoxin as an electron carrier. It is virtually completely reduced because of high redox potentials. Chemically the protein is different from ferredoxin. When bleaching of the visible spectrum. Rubredoxin undergoes a very slow bleaching while the ferredoxin reacts within seconds. Rubredoxin represents a distinct class of electron transfer proteins Rubredoxin form the hyperthermophilic archeon Pyrococcus Furiosus. It is a part of a three-component system that carries out the oxidation of alkanes to alkanol. Their small size is beneficial when it comes to ease of isolation and stability. Oxidized Rubredoxin has distinctive UV-visible absorption with an intense band at 280 nm, 385 nm and 490nm that arises from the charge transfer from cysteinyl thiolate to Fe 3+. The Fe 3+/2+  had a resolution that was 1.8 Å.