Fig. 5: Analysis of Pi mobility inside the catalytic center.
a Pi(B), in stick and ball format (phosphorus is orange, oxygen is red), in a crystal structure complex with AtPFA-DSP149–215 (PDB accession code 7MOL) obtained in the absence of mercaptoethanol (see text). Broken lines depict polar interactions of Pi(B) (≤3.2 Å) with nearby residues (nitrogens are blue). The Fo-Fc electron density map (green mesh) is contoured at 5σ. b corresponding rendering of the ligand–protein interactions created by Ligplot+. c Pi(B) from panel (a) is superimposed upon Pi(A) (taken from Fig. 2a); the P-loops of the corresponding proteins are colored gray for Pi(B) and light brown/dark brown for Pi(A). Note the two conformations of Cys150, one of which may form a disulfide bond (see panel a). d, e the movement of the phosphorus atom is indicated by the orange trace, and each of the oxygen atoms of Pi(A) were arbitrarily colored either purple, light pink, red or green; this color scheme illustrates the predicted movements of each atom during molecular dynamics simulations, with reference to the plane of the backbone residues of the P-loop (blue rectangle; residues 151–156). Horizontal bars illustrate the switching between Pi poses A (black) and B (white). The coloration in this simulation has been transferred to Pi(B) in panels (c) and (e). Three additional replicates of the data in panel (d) are provided in Supplementary Fig. S8, and the initial 1000 ns of each of these aspects of all four simulations are animated in Supplementary Movies 1, 2, 3 and 4. Source data are provided as a Source Data file.
