Nucleobase carbonyl groups are poor Mg$^{2+}$; monovalent ions; ribozyme; ribosome; lanthanides inner-sphere binders but excellent monovalent ion binders—a critical PDB survey - Archive ouverte du site Alsace Access content directly
Journal Articles RNA Year : 2019

Nucleobase carbonyl groups are poor Mg$^{2+}$; monovalent ions; ribozyme; ribosome; lanthanides inner-sphere binders but excellent monovalent ion binders—a critical PDB survey

Abstract

Precise knowledge of Mg$^{2+}$ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg$^{2+}$ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg$^{2+}$ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg$^{2+}$ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of “prior-knowledge” nucleobase Mg$^{2+}$ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg$^{2+}$ binding sites are fewer than expected since many of those are associated with misidentified Na$^+$ or K$^+$. We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg$^{2+}$ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg$^{2+}$ stereochemistry is observed, alternative placement of Na$^+$, K$^+$, or Ca$^{2+}$ must be considered. We also critically examine the use of lanthanides (Yb$^{3+}$, Tb$^{3+}$) as Mg$^{2+}$ substitutes in crystallography experiments.
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hal-02119072 , version 1 (11-06-2024)

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Filip Leonarski, Luigi d'Ascenzo, Pascal Auffinger. Nucleobase carbonyl groups are poor Mg$^{2+}$; monovalent ions; ribozyme; ribosome; lanthanides inner-sphere binders but excellent monovalent ion binders—a critical PDB survey. RNA, 2019, 25 (2), pp.173-192. ⟨10.1261/rna.068437.118⟩. ⟨hal-02119072⟩

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