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Figure 4
The active site and RNA-binding groove of ALSV NS3-Hel. (a) Invariant residues in the active site of ALSV NS3-Hel are shown as stick models (blue); their counterparts in the superimposed ZIKV NS3-Hel (PDB entry 5y6m; Yang et al., 2018BB32) are shown in gray. The bound ligands ADP (orange), AlF3 (cyan) and manganese ion (purple) are also shown. Residues from ALSV NS3-Hel are annotated in italics. (b) Structural superimposition of the P-­loops of apo ALSV NS3-Hel (blue), apo DENV4 NS3-Hel (red), DENV4 NS3-Hel complexed with RNA and AMPPNP (green), apo ZIKV NS3-Hel (orange) and ZIKV NS3-Hel complexed with RNA (yellow). (c) A model of an ALSV NS3-Hel–RNA complex. The RNA was modeled into the ALSV NS3-Hel structure by superimposition with the DENV4 NS3-Hel–RNA complex (PDB entry 2jlv; Luo et al., 2008BB18). ALSV NS3-Hel is colored by domain: D1, light blue; D2, light green; D3, pink. Residues that were predicted to contact RNA are colored blue and shown as stick models. (d) Aromatic residues located at the 5′ end of the model RNA. Residues from ALSV NS3-Hel are shown as magenta stick models and their structural counterparts in DEVN4 NS3-Hel are shown as cyan stick models. RNA is shown a a red stick model.

IUCrJ
Volume 7| Part 3| May 2020| Pages 375-382
ISSN: 2052-2525
https://doi.org/10.1107/S2052252520003632