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Figure 3
8AZA and W1. (a) 8AZA monoanion (orange) bound in the active site viewed from the peroxo hole. 2mFo − DFc neutron density map is shown in grey at the 1.0σ level for active site residues. Amino acids shown in yellow and magenta belong to different UOX protomers. Nitro­gen, oxygen and deuterium atoms are shown in blue, red and wheat, respectively. Hydrogen bonds are shown as cyan broken lines. Residues labelled with an asterisk indicate that they belong to a different UOX protomer. (b) Sliced-surface view of W1 bound in the peroxo hole located above the flat binding pocket occupied by 8AZA. The molecular surface is coloured according to the electrostatic potential with positive potential shown as shades of blue. 2mFo − DFc neutron density map for W1 is shown at the 1.5σ level. (c) W1 is present as a neutral H2O molecule. 2mFo − DFc electron density map shown in blue at the 3.0σ level clearly define the W1O position. An omit mFo − DFc neutron map calculated only with W1O contribution indicates the presence of two deuterons (D1, D2) as suggested by the elongated positive density (in green at the +3.0σ level) next to the oxygen atom. (d) W1 is sandwiched between Thr57* and Asn254. The latter is modelled in two conformations that refine at 0.8 (major) and 0.2 (minor) occupancy, respectively. W1 is oriented such that its D2 atom forms an O—H⋯π hydrogen bond with 8AZA. Useful parameters to describe this type of interaction are the O–m distance (broken grey line), where m is the midpoint of the six-membered pyrimidine ring, the ω(O) angle between the O⋯m line and the ring normal (thin continuous black line), as well as the O—D2⋯m angle (Steiner & Koellner, 2001BB60). These values are 3.64 Å, 23.8° and 141°, respectively.

IUCrJ
Volume 8| Part 1| January 2021| Pages 46-59
ISSN: 2052-2525
https://doi.org/10.1107/S2052252520013615