Cited by 29RNA and protein synthesis mechanismsEnzyme Structure and FunctionProtein Structure and Dynamics

Deflating the RNA Mg 2+ bubble: stereochemistry to the rescue!

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Auffinger, Pascal, Ennifar, Eric, D'Ascenzo, Luigi·2021·RNA

Published version of a preprint

Abstract

Proper evaluation of the ionic structure of biomolecular systems through X-ray and cryo-EM techniques remains challenging but is essential for advancing our understanding of the underlying structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg 2+ in deposited structures due to assignment errors finding their origin in improper consideration of stereochemical rules. Herein, to tackle such issues, we reevaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure. We establish that stereochemical principles need to be carefully pondered when examining ion binding features, even when K + anomalous signals are available as is the case for the 6QNR PDB entry. For ribosomes, assignment errors can result in misleading conceptions of their solvent structure. For instance, present stereochemical analysis results in a significant decrease of the number of assigned Mg 2+ in 6QNR, suggesting that K + and not Mg 2+ is the prevalent ion in the ribosome first solvation shell. We stress that the use of proper stereochemical guidelines in combination or not with other identification techniques, such as those pertaining to the detection of transition metals, of some anions and of K + anomalous signals, is critical for deflating the current Mg 2+ bubble witnessed in many ribosome and other RNA structures. We also stress that for the identification of lighter ions such as Mg 2+ , Na + , …, for which no anomalous signals can be detected, stereochemistry coupled with high resolution structures (<2.4 Å) remains the best currently available option.

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Crossref · 10.1261/rna.076067.120

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  • A subset of ribosomally associated K+ is thought to be localized deep within the macromolecular structure where residence times may approach the lifetime of the folded ribosomal subunits.

    “A subset of ribosomally associated K+ is thought to be localized deep within the macromolecular structure where residence times may approach the lifetime of the folded ribosomal subunits.54”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [54]

    The paper’s Abstract makes the contrary distinction: it describes K+ as weakly coordinating and says that Mg2+ bound in the rRNA core may have residence times approaching the lifetime of folded ribosomal subunits. It does not assign that long residence time to K+. No page number is available in our copy. (LLM, conf=0.90)

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  • >3000 cation-binding sites were visualized in the Thermus thermophilus 70S ribosome and assigned as Mg2+, but those assignments have been challenged on experimental and stereochemical grounds.

    “As an upper limit, > 3000 cation-binding sites were visualized in the Thermus thermophilus 70S ribosome51 and assigned as Mg2+, but those assignments have been challenged on both experimental52 and stereochemical54 grounds.”
  • With ∼3 × 10^4 ribosomes per fL of cell volume and up to ∼400 K+ site-specifically bound per ribosome, ribosomes may bind up to ∼1.2 × 10^7 K+ ions (∼10% of the cell quota) in these sites alone.

    “With ∼3 × 104 ribosomes per fL (10–15 liters) of cell volume,56 and up to ∼400 K+ site-specifically bound per ribosome,54 ribosomes may bind up to ∼1.2 × 107 K+ ions (∼10% of the cell quota) in these sites alone.”
  • Stereochemical considerations argue that many sites assigned as Mg2+ in ribosome structures may be occupied instead by K+.

    “Stereochemical considerations argue that many sites assigned as Mg2+ (Figure 4c) may be occupied instead by K+ (Figure 4d).52,54”
  • Further analysis using stereochemical constraints refined these estimates and assigned ~400 monovalent ions and ~100 Mg2+ in the first solvation shell.

    “Further analysis using stereochemical constraints refined these estimates further and assigned ∼400 monovalent ions and ∼100 Mg2+ in the first solvation shell.54”

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Cited by

Sorted by citations

Authors
Auffinger, P., Ennifar, E., & D'Ascenzo, L.
Affiliations
Centre National de la Recherche Scientifique (FR)
Corresponding author
Auffinger, Pascal
Venue
RNA
Published
2020-12-02
Volume
27
Issue
3
Pages
243-252
ISSN
  • 1355-8382 (ISSN-L)
  • 1469-9001
OpenAlex
W3107309388
Cited by
29
References
0
Citations by year
2026: 3 · 2025: 8 · 2024: 4 · 2023: 5 · 2022: 5 · 2021: 4
FWCI
1.12
Type
journal article
Language
en
Open access
Locations
  • RNA (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
  • HAL (submittedVersion, cc-by-nc)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
magnesium binding, resonant scattering, potassium ions, first solvation shell

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