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Cited by 39Enzyme Structure and FunctionDNA and Nucleic Acid ChemistryRNA and protein synthesis mechanisms

Nucleobase carbonyl groups are poor Mg2+inner-sphere binders but excellent monovalent ion binders—a critical PDB survey

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Leonarski, Filip, D'Ascenzo, Luigi, Auffinger, Pascal·2019·RNA
DOI 10.1261/rna.068437.118PMC PMC6348993
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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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  • Ribosome-bound K+ is coordinated by oxygen from phosphodiester linkages, carbonyl groups, ribosomal proteins, and water, and by nitrogen from the nucleobases.

    “Ribosome-bound K+ is coordinated by oxygen (from phosphodiester linkages, carbonyl groups, ribosomal proteins, and water) and nitrogen from the nucleobases.55”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [55]

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Cited by

Sorted by citations

Authors
Leonarski, F., D'Ascenzo, L., & Auffinger, P.
Affiliations
Centre National de la Recherche Scientifique (FR)
ORCID
Venue
RNA
Publisher
Cold Spring Harbor Laboratory
Published
2018-11-08
Volume
25
Issue
2
Pages
173-192
ISSN
  • 1355-8382 (ISSN-L)
  • 1469-9001
DOI
10.1261/rna.068437.118
PMC
PMC6348993
OpenAlex
W2899690113
Cited by
39
References
0
Citations by year
2026: 2 · 2025: 5 · 2024: 3 · 2023: 3 · 2022: 10 · 2021: 6 · 2020: 4 · 2019: 4 · 2018: 1
FWCI
1.37
Type
journal article
Language
en
Open access
Locations
  • RNA (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by-nc)
  • DORA PSI (Paul Scherrer Institute) (submittedVersion, other-oa)
  • HighWire Press Open Archive (submittedVersion)
Funders
French National Research Agency (ANR-15-CE11-0021-01)
Topics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
magnesium binding, inner-sphere coordination
MeSH terms
Binding Sites, Calcium, Magnesium, Potassium, Ribosomes, Sodium, Terbium, Ytterbium, RNA, Catalytic, Crystallography, X-Ray, Catalytic Domain, Databases, Protein

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