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Figure 5
Asn254 heterogeneity. (a) Close-up of the β5–β8 region highlighting an alternative conformation for the Pro253–Lys255 tripeptide. Strands are shown as tubes and the stretch connecting β7 to β7′ as sticks. Deuterium atoms have been omitted for clarity. The main conformation for the Pro253–Lys255 tripeptide is shown in yellow and the second conformation is represented in dark grey for reference. Difference mFo − DFc electron density maps at the +3.0σ and −3.0σ levels calculated after refinement without the minor conformation included in the model are shown in green and red, respectively. The alternative conformation stretch explains the residual density well. (b) Feature-enhanced 2mFo − DFc map (FEM) for the Pro253–Lys255 tripeptide and neighbouring residues. Colour codes are the same as in (a). The solvent molecule W′ is hydrogen bonded to the oxygen atom of the Asn254 amide in the minor conformation. (c) 2D contour plot for Asn254 torsion angles from MD simulations highlighting four main clusters represented by different colours (green, yellow, aqua and dark grey). Red squares within the yellow and dark grey clusters identify experimental torsion angles for the major (179°, −192°) and minor (272°, 81°) Asn254 conformations, respectively. (d)–(g) Representative structures of each torsion angle cluster identified by the simulations: (d) yellow, (e) dark grey, (f) aqua, (g) green. 8AZA, Thr57*, Asn254, W1 and other water molecules at hydrogen-bond distance are shown as sticks. Asn254 is colour-coded according to the cluster to which it belongs. Hydrogen bonds are shown by broken cyan lines.

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