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Figure 3
Structural features of G*O complexes. (a) Global side-by-side comparison of G*Odark (left) versus G*Olight (right). DNA and protein are shown in a tube representation, with tube thickness proportional to normalized B factor. Structures are also coloured by normalized B factor, with the colour scale below the figure. B factors were normalized following the scheme described previously (Carugo, 2022View full citation). An oval discontinuous line marks the position of the G/P-rich loop. (b) Comparison of the G*Odark (blue) versus the G*Olight (orange) active site. DNA/protein residues are shown as stick diagrams, while water molecules corresponding to G*Odark are shown as blue spheres and those for G*Olight as orange spheres. A 3σ-contoured σA-weighted Fo(G*Olight) − Fc(G*Odark) DED map is superposed over the structural models. Positive DED peaks are shown in green; no negative peaks could be visualized. (c) Detail of the exosite of G*Odark versus G*Olight shown as in (b). (d) Detail of the active site of G*Olight (orange) versus the previously published, catalytically inert, GOK249Q complex (green, PDB entry 6w0m). DNA/protein residues and water molecules are depicted as in (b). A 1σ-contoured σA-weighted 2Fo − Fc composite omit map of G*Olight is superposed over the DNA to highlight the presence of oG within the active site. (e) Detail of the exosite of G*Olight versus GOK249Q, shown as in (d). A calcium ion present in G*Olight but not in GOK249Q is represented by a green sphere, with a 1σ-contoured σA-weighted 2Fo − Fc composite omit map shown in orange.

IUCrJ
Volume 12| Part 5| September 2025| Pages 515-522
ISSN: 2052-2525
https://doi.org/10.1107/S2052252525006062