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. 2023 Apr 26;51(10):4713–4725. doi: 10.1093/nar/gkad309

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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 5. — Active site of Klenow fragment exonuclease complexed with DNA·DNA (A) SpDNA·DNA (B) and RpDNA·DNA (C). The two-Mg²⁺ centered active site is shown. The nucleophilic water molecule (WAT_Nuc) is coordinated to one of the Mg²⁺ ion (in pink). The reactive distance (i.e. d_Nuc) between nucleophile (i.e. WAT_Nuc) and electrophile (i.e. P atom) is reported and taken as a key geometrical description to evaluate the correct geometry of Exonuclease reactive active site, a well-known arrangement (25). (D) Frequency Distribution of d_Nuc length calculated for the different systems under investigation. Three additional replicas have been performed to explore the reproducibility of these findings. The corresponding histograms nearly overlap and are not shown for clarity reasons, but are available upon request.