Extended Data Fig. 8: Electron density maps around pyridoxal-phosphate (PLP) in the L-propargylglycine (PG)-containing (NIAU)2 crystal structure.
From: d-cysteine impairs tumour growth by inhibiting cysteine desulfurase NFS1
The 2Fo-DFc (blue; contoured at 0.5 sigma) and Fo-DFc (orange; 2.5 sigma) difference maps were calculated after 5 refinement macrocycles in Phenix of the model from which the PG-PLP, the sidechain of Lys258, and residues 377-387 were excluded (PDB ID: 8TVT). While the density for the loop is weak, it was possible to build backbones of residues Gly378-Cys381 and Ala384-Glu387. Most of the sidechains in this region were not visible and were not modeled. The Fo-DFc map clearly shows that Lys258 is not covalently bound to PLP, thus defining PG-PLP as an external aldimine. There appears to be density at low level to allow placing the sidechain of Cys381 in one possible conformation, where it points toward the PG sidechain.
