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Figure 2
Definition of the geometrical parameters describing the stereochemistry of the attack of an enzyme hydroxyl nucleophile on the amide group electrophile of L-asparagine. The atoms are labeled as in a real L-asparaginase case. For some of the general definitions, Oγ would correspond to Onuc and Cγ to Cel. When the pyramidalization Δ of the amide group is significant, the projection of the Cγ atom on the plane of its O/N/C substituents is marked as C′ (black point below Cγ). αBD is the Bürgi–Dunitz angle Onuc–Cel=O; αFL is the Flippin–Lodge angle defined as 180° − P–C′=O, where P is a projection of Onuc on the electrophile plane; αLW is the Lubkowski–Wlodawer angle Onuc–Cel–P′, where P′ is a projection of Onuc on plane Ω, which is perpendicular to the electrophile plane through the C=O bond; Φattack is the Onuc–O=C′—C torsion angle; d is the Onuc⋯Cel distance; dP is the P⋯C′ distance; the degree of pyramidalization Δ is defined as the deviation of Cel from the plane of its O/N/C substituents, i.e. C′⋯Cel; Δ > 0 when Cel deviates toward Onuc.

IUCrJ
Volume 13| Part 2| March 2026| Pages 132-145
ISSN: 2052-2525
https://doi.org/10.1107/S2052252525010826