PapB is a highly promiscuous radical S-adenosyl-l-methionine (rSAM) enzyme that can install thio(seleno)ether crosslinks in diverse substrates. The substrate scope of this enzyme has been largely underexplored, with most studies only considering the native Cys-X3-Asp thioether motif. The redox stability of thioether crosslinks makes PapB an attractive candidate for use as a biotechnological tool. The results demonstrated here show that PapB will process nested and in-line crosslinks with varied distances between each crosslinking site. Further, we demonstrate that PapB will process non-peptidic substrates and install the thioether crosslink at predictable positions.