Reconsideration of the P-clusters in VFe proteins using the bond-valence method: towards their electron transfer and protonation.

P-clusters have been statistically analysed using the bond-valence sum (BVS) method together with weighting schemes. The crystallographic data come from the VFe proteins deposited in the Protein Data Bank (PDB) with high resolutions of better than 1.35 Å. Calculations show that the formal oxidation state of a P¹⁺ cluster can be assigned as 2Fe³⁺6Fe²⁺ with high electron delocalization, giving the same oxidation state as that of P^N clusters in VFe proteins. Further comprehensive comparisons of the bond distances suggest that the hydroxyl groups of the β-153 serine residues in P¹⁺ and P^N clusters are in the protonated state, where the Fe6 atoms have the same oxidation state as Fe²⁺. During the transition from P^N to P¹⁺, cleavage of the Fe6-S1 bond is accompanied by the formation of a weak coordination between the Fe6 atom and the hydroxyl group of the β-153 serine residue in the P¹⁺ cluster of the VFe protein. Similarly, oxidation of P^N to P¹⁺/P²⁺ clusters corresponds to the coordination of Fe6(II) by the hydroxyl group of the β-188 serine residue and of Fe5(II) by the peptide amine group of the α-88 cysteine residue in the MoFe protein of Azotobacter vinelandiis without electron and proton transfers.