Figure 3.
The catalytic site of SARS–CoV-2 3CL Mpro. X-ray diffraction data provide no information on the positions of hydrogen atoms as shown in A, whereas neutron diffraction data provide direct observation of deuterium atoms as shown in B. A, the 2Fo − Fc electron density map is contoured at 2.0 σ level (gray mesh). Distances between the heavy atoms in Ångstroms illustrate possible hydrogen bonds (black dashed lines). B, the 2Fo − Fc nuclear density map is contoured at 2.0 σ level (violet mesh), allowing visualization of the actual protonation states and hydrogen-bonding interactions shown as black dashed lines (deuterium–oxygen distances are shown in Ångstroms). Deuterium atoms are colored yellow, whereas hydrogen atoms are colored light gray.