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. 2019 Dec 27;18:137–152. doi: 10.1016/j.csbj.2019.12.003

Fig. 3.

Fig. 3

Molecular interactions of 8-oxo-7,8-dihydroguanosine (8-oxoG) in the active binding tunnel of PNPase. A) Key interactions between PNPase residues and 8-oxoG at position P4. B) Interaction free energy between each residue and guanosine (G) or 8-oxoG at position P4. Interaction is decomposed into polar (dark shade) and nonpolar (light shade) contributions. Only residues with an average interaction free energy less than −1.0 kcal/mol are shown. C) Key interactions between PNPase residues and 8-oxoG at position P8. D) Interaction free energy between each residue and G or 8-oxoG at position P8. E) Key interactions between PNPase residues and 8-oxoG at position P9. F) Interaction free energy between each residue and G or 8-oxoG at position P9. The interaction-free energies are obtained from three 50 ns MD simulations of the PNPase – RNA complex. Error bars plotted as ± one standard deviation.