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Figure 2
Mpro/C145A–substrate interactions for induced fit of substrate. (a) Main-chain hydrogen-bond interactions between Mpro and the peptide substrate (shown as orange and green C atoms, respectively). Hydrogen bonds are shown as dotted lines. Distances are in Å. (b) Hydrogen-bond interactions between peptide P1 Gln with the S1 subsite and the catalytic site. Water molecules are shown as red spheres. (c) Superposition of Mpro/C145A–substrate with the substrate-free Mpro neutron crystal structure (light blue; PDB entry 7jun) showing the scissile bond in relation to the catalytic Cys145–His41 zwitterion. Superposition was by a least-squares fit to Cα atoms of protomer A. (d) Induced fit of Mpro/C145A to the peptide substrate by the rearrangements of side chains in the S2 and S4 subsite.

IUCrJ
Volume 8| Part 6| November 2021| Pages 973-979
ISSN: 2052-2525
https://doi.org/10.1107/S2052252521010113