ArticleNucleic acids research2020
Conformation-dependent restraints for polynucleotides: the sugar moiety.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 19 citations in OpenAlex.
- Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields.Acta crystallographica. Section D, Structural biology · 2026Article
- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields.bioRxiv : the preprint server for biology · 2025Article
- When will RNA get its AlphaFold moment?Nucleic acids research · 2023Article
- Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method.Acta crystallographica. Section D, Structural biology · 2023Article
- Mechanism of RNA polymerase I selection by transcription factor UAF.Science advances · 2022Article
- New restraints and validation approaches for nucleic acid structures in PDB-REDO.Acta crystallographica. Section D, Structural biology · 2021Article
- Crystal structure of Z-DNA in complex with the polyamine putrescine and potassium cations at ultra-high resolution.Acta crystallographica Section B, Structural science, crystal engineering and materials · 2021Article
- Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models.Protein science : a publication of the Protein Society · 2021Article
- Structural Insights Into the 5'UG/3'GU Wobble Tandem in Complex With BaFrontiers in molecular biosciences · 2021Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Stereochemical restraints are commonly used to aid the refinement of macromolecular structures obtained by experimental methods at lower resolution. The standard restraint library for nucleic acids has not been updated for over two decades and needs revision. In this paper, geometrical restraints for nucleic acids sugars are derived using information from high-resolution crystal structures in the Cambridge Structural Database. In contrast to the existing restraints, this work shows that different parts of the sugar moiety form groups of covalent geometry dependent on various chemical and conformational factors, such as the type of ribose or the attached nucleobase, and ring puckering or rotamers of the glycosidic (χ) or side-chain (γ) torsion angles. Moreover, the geometry of the glycosidic link and the endocyclic ribose bond angles are functionally dependent on χ and sugar pucker amplitude (τm), respectively. The proposed restraints have been positively validated against data from the Nucleic Acid Database, compared with an ultrahigh-resolution Z-DNA structure in the Protein Data Bank, and tested by re-refining hundreds of crystal structures in the Protein Data Bank. The conformation-dependent sugar restraints presented in this work are publicly available in REFMAC, PHENIX and SHELXL format through a dedicated RestraintLib web server with an API function.
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