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. 2023 Apr 28;51(10):5255–5270. doi: 10.1093/nar/gkad314

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© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 6. — Overall visualization of fragments bound to NendoU. (A) Overall view of all NendoU sites bound to fragments in multiple orientations. All chains containing fragments were supperposed into one, colored as blue surface, while adjacent chains of biological units are colored in shades of gray. Colored squares highlight the cluster of fragments identified. (B) Detailed view of cluster 1 (active site) showing citrate, multiple fragment contacts and the RNA binding mode. (C) Detailed view of cluster 2 showing multiple fragment contacts and the oligomerization interface. (D) Detailed view of cluster 3, showing multiple fragment contacts and the RNA binding mode. (E) Detailed view of cluster 4, showing multiple fragment contacts with NendoU. In all, the NendoU surface is colored in blue, fragments are depicted as sticks or spheres with yellow carbons, while interacting NendoU residues are depicted as gray carbon sticks. RNA carbons are colored in orange, and coordinates were obtained from PDB 7TJ2.