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Key states involved in reaction path B of the papain-catalyzed hydrolysis of APGNA. The geometries were optimized at the QM/MM(B3LYP/6-31G*:AMBER) level. The key distances are given in Å. Carbon, oxygen, nitrogen, sulfur, and hydrogen atoms are colored in green, red, blue, yellow, and white, respectively. The backbone of the protein is rendered in orange. The QM atoms are represented as balls and sticks, and the surrounding residues are rendered as sticks or lines.
