Fig. 4: In silico analysis of NifB-co and FeMo-co binding to NifX and NifEN.
From: Trafficking of a nitrogenase FeMo-cofactor assembly intermediate
a, Using Boltz-2, a single NifB-co is consistently predicted to bind inside NifE at residue C250E, consistent with FeMo-co binding to NifDK (Fig. 2g). b, NifB-co-bound NifEN shows two distinct pathways from the protein surface to the internal conversion site, one close to the NifE–NifN interface (left) and another between the three domains of NifE (right). c, In the homologous MoFe protein (yellow), both of these pathways are blocked by the extended N terminus of NifD that differs strongly from the NifB-co-binding N terminus of nNifE. d, Only if two NifB-co clusters are used with Boltz-2 does the second one bind to the receiving site through cysteine C15E and C20E. In this prediction, the N terminus of NifE is not tightly folded onto the cofactor, making it more accessible from the outside. e, With inclusion of homocitrate, the ligand clusters strongly around the free apical iron of the NifB-co in the conversion site. f, If FeMo-co is used with homocitrate instead of NifB-co, the prediction becomes highly consistent, with homocitrate binding to the terminal Mo ion, surrounded by positively charged residues. g, Only when a third NifB-co is included in the Boltz-2 prediction is the transport site at H34X of NifX also occupied, consistent with the experimentally observed binding mode (Fig. 3).
