Acta Crystallogr D Struct Biol. 2025 Feb 1. doi: 10.1107/S2059798325000415. Online ahead of print.
ABSTRACT
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 PN 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 PN clusters are in the protonated state, where the Fe6 atoms have the same oxidation state as Fe2+. During the transition from PN 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 PN 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.
PMID:39841458 | DOI:10.1107/S2059798325000415
