Bond‐valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins

• Published in: Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2020-05, Vol.76 (5), p.428-437
• Main Authors: Jin, Wan-Ting, Yang, Min, Zhu, Shuang-Shuang, Zhou, Zhao-Hui
• Format: Article
• Language: English
• Subjects: Binding Sites; bond‐valence method; Catalytic Domain; Coenzymes - chemistry; Cofactors; Crystal structure; Crystallography; Crystals; Databases, Protein; Error analysis; Histidine; Iron; Iron - chemistry; Mathematical analysis; Models, Molecular; Molybdenum; Molybdenum - chemistry; Molybdoferredoxin - chemistry; nitrogenase cofactors; oxidation state; protein structure; Proteins; Selenium; Vanadium; Vanadium - chemistry
• ISSN: 2059-7983; 0907-4449; 2059-7983; 1399-0047
• DOI: 10.1107/S2059798320003952

The bond‐valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe7S9C(Cys)(HHis)[R‐(H)homocit] (where H4homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO‐bound and selenium‐substituted FeMo cofactors and O(N)H‐bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms. The bond‐valence method was performed on 51 crystallographic data sets from nitrogenase proteins, indicating the presence of molybdenum(III) in FeMo cofactors and of vanadium(III) with more reduced iron complements in FeV cofactors.