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. 2023 Sep 16;14:5752. doi: 10.1038/s41467-023-41533-x

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — Protonation state of Y244 in the P_R (A) and O (B) states. The post translationally modified Y244 forms a H-bonding network with the OH group of the farnesyl side chain of heme a₃, a water molecule (W¹) and T316. In the P_R state, an additional water, W², is recruited into the heme a₃/Cu_B binuclear center (BNC) to stabilize the tyrosinate configuration of Y244. This water is absent in the O state reported here, as evident in the 2F_O-F_C electron density map (contoured at 1.0σ) shown in the lower inset, signifying that Y244 is in the neutral protonated state. For clarity the BNC ligands are not shown. The oxygen atom and hydrogen atoms are shown as red and white spheres.