ArticleProtein science : a publication of the Protein Society2016
Geometry of guanidinium groups in arginines.
Article in Protein science : a publication of the Protein Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 11 citations in OpenAlex.
- S-Adenosylmethionine-Dependent Methylation, Protein Arginine Methyltransferases and Cardiovascular Diseases.Biomolecules · 2026Review
- Protein Recognition and Assembly by a Phosphocavitand.Journal of the American Chemical Society · 2025Article
- X-ray crystallographic and hydrogen deuterium exchange studies confirm alternate kinetic models for homolog insulin monomers.PloS one · 2025Article
- In situ ligand restraints from quantum-mechanical methods.Acta crystallographica. Section D, Structural biology · 2023Article
- Arginine off-kilter: guanidinium is not as planar as restraints denote.Acta crystallographica. Section D, Structural biology · 2020Article
- Interfacial plasticity facilitates high reaction rate ofProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Validation and extraction of molecular-geometry information from small-molecule databases.Acta crystallographica. Section D, Structural biology · 2017Article
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
The restraints in common usage today have been obtained based on small molecule X-ray crystal structures available 25 years ago and recent reports have shown that the values of bond lengths and valence angles can be, in fact, significantly different from those stored in libraries, for example for the peptide bond or the histidine ring geometry. We showed that almost 50% of outliers found in protein validation reports released in the Protein Data Bank on 23 March 2016 come from geometry of guanidine groups in arginines. Therefore, structures of small molecules and atomic resolution protein crystal structures have been used to derive new target values for the geometry of this group. The most significant difference was found for NE-CZ-NH1 and NE-CZ-NH2 angles, showing that the guanidinium group is not symmetric. The NE-CZ-NH1 angle is larger, 121.5(10)˚, than NE-CZ-NH2, 119.2(10)˚, due to the repulsive interaction between NH1 and CD1 atom.
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