ArticleIUCrJ2014
Do we see what we should see? Describing non-covalent interactions in protein structures including precision.
Article in IUCrJ, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 63 citations in OpenAlex.
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- Generation and modulation of catalytically relevant states of a dye-decolourizing peroxidase using time-resolved serial femtosecond crystallography with drop-on-chip mixing and X-ray-driven reduction.Acta crystallographica. Section D, Structural biology · 2026Article
- Can ferric-oxyl excited states explain elongated iron-oxygen bonds in heme peroxidase catalytic intermediates?Nature communications · 2026Article
- Damage before destruction? X-ray-induced changes in single-pulse serial femtosecond crystallography.IUCrJ · 2025Article
- A database overview of metal-coordination distances in metalloproteins.Acta crystallographica. Section D, Structural biology · 2024Article
- Structure of a ribonucleotide reductase R2 protein radical.Science (New York, N.Y.) · 2023Article
- Error estimates in atom coordinates and B factors in macromolecular crystallography.Current research in structural biology · 2023Review
- Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation.Current research in structural biology · 2023Article
- Crystal Structure of the Human Copper Chaperone ATOX1 Bound to Zinc Ion.Biomolecules · 2022Article
- The four Rs and crystal structure analysis: reliability, reproducibility, replicability and reusability.Journal of applied crystallography · 2022Article
- Raw diffraction data are our ground truth from which all subsequent workflows develop.Acta crystallographica. Section D, Structural biology · 2022Article
- Uses and Abuses of the Atomic Displacement Parameters in Structural Biology.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Decline of protein structure rigidity with interatomic distance.BMC bioinformatics · 2021Article
- Correlated Motions in Structural Biology.Biochemistry · 2021Review
- Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure-function studies.Acta crystallographica. Section A, Foundations and advances · 2021Article
- Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems.The journal of physical chemistry. B · 2020Article
- Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase.Nature communications · 2020Article
- Structural determination of Enzyme-Graphene Nanocomposite Sensor Material.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The power of X-ray crystal structure analysis as a technique is to 'see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this 'seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and α-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.
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