Home How to Name Atoms in Phosphates, Polyphosphates, their Analogues, and Transition State Analogues for Enzyme-catalysed Phosphoryl Transfer Reactions
Article Publicly Available

How to Name Atoms in Phosphates, Polyphosphates, their Analogues, and Transition State Analogues for Enzyme-catalysed Phosphoryl Transfer Reactions

Published/Copyright: March 19, 2016
Download Article (PDF)
Become an author with De Gruyter Brill
Author Information
Chemistry International
From the journal Chemistry International Volume 38 Issue 2

Procedures are proposed for the naming of individual atoms, N, P, O, etc., in phosphate esters, amidates, thiophosphates, polyphosphates, their mimics, and analogues of transition states for enzyme-catalysed phosphoryl transfer reactions. Their purpose is to enable scientists in very different fields, e.g. biochemistry, biophysics, chemistry, computational chemistry, crystallography, molecular biology, NMR, etc., to share standard protocols for the labelling of individual atoms in complex molecules. This will facilitate clear and unambiguous descriptions of structural results and scientific intercommunication concerning them. At the present time, perusal of the Protein Data Bank (PDB) and other sources shows that there is a limited degree of commonality in nomenclature but a large measure of irregularity in more complex structures. There appears to be no common ground with nomenclature used in computational work or in NMR. The recommendations described herein adhere to established practice as closely as possible, in particular to IUPAC and IUBMB recommendations, and to “best practice” in the PDB, especially to its atom labelling of amino acids, and particularly to Cahn-Ingold-Prelog rules for stereochemical nomenclature. They are designed to work in complex enzyme sites for binding phosphates, but also to have utility for non-enzymatic systems. Above all, the recommendations are designed to be clear, easy to assimilate, and convenient to use.

Comments by 30 June 2016.

Corresponding author: G. Michael Blackburn, <>

www.iupac.org/project/2013-039-2-300

Published Online: 2016-3-19
Published in Print: 2016-3-1

©2016 by Walter de Gruyter Berlin/Boston

Articles in the same Issue

  1. Masthead - Full issue pdf
  2. Guest Editorial
  3. Outer Limits: Pushing the Extremities
  4. Contents
  5. Officer’s Column
  6. Secretary General’s Column
  7. Features
  8. The Three-letter Element Symbols:
  9. Procedures for the Naming of a New Element
  10. The Chemical Structure Association Trust
  11. IUPAC Wire
  12. Discovery and Assignment of Elements with Atomic Numbers 113, 115, 117 and 118
  13. Open Data in a Big Data World
  14. UN Secretary General Appoints ICSU Executive Director to Special Advisory Group on the SDGs
  15. Project Place
  16. Company Associates Reengineering Project
  17. Postgraduate Course in Polymer Science, Prague, Czech Republic
  18. Critically Evaluated ESR (EPR) Spectra of Important Polymerization-related Radicals
  19. Which Elements Belong in Group 3 of the Periodic Table?
  20. Making an imPACt
  21. Discovery of the elements with atomic numbers Z = 113, 115 and 117 (IUPAC Technical Report)
  22. Discovery of the element with atomic number Z = 118 completing the 7th row of the periodic table (IUPAC Technical Report)
  23. Glossary of terms used in computational drug design, part II (IUPAC Recommendations)
  24. Standard electrode potentials involving radicals in aqueous solution: inorganic radicals (IUPAC Technical Report)
  25. Maritime pollutants in shipping and commercial European ports based on relevant physical and biogeochemical environmental parameters (IUPAC Technical Report)
  26. Latest Updates from PAC Conferences & More—Brief
  27. IUPAC Provisional Recommendations
  28. Glossary of Terms Used in Developmental and Reproductive Toxicology
  29. How to Name Atoms in Phosphates, Polyphosphates, their Analogues, and Transition State Analogues for Enzyme-catalysed Phosphoryl Transfer Reactions
  30. Comprehensive Definition of Oxidation State
  31. Stamps International
  32. Berzelius and the Chemical Alphabet
  33. Conference Call
  34. Latin American Pesticide Residue Workshop—Food and Environment
  35. Ecological Risk Assessment
  36. Where 2B & Y
  37. New Chemistries for Phytomedicines and Crop Protection Chemicals
  38. Function Through Disorder: Intrinsically Disordered Proteins in Biology and Medicine
  39. Phosphorus Chemistry
  40. Self-assembly in the World of Polymers
  41. Solubility Phenomena
  42. Blood-Biomaterial Interactions
  43. CODATA-RDA School of Research Data Science
  44. 28th National [Turkish] Chemistry Congress with International Participation
  45. The Power of Norms
  46. Selenium Research (Se2017)
  47. Mark Your Calendar
https://doi.org/10.1515/ci-2016-0221

Articles in the same Issue

  1. Masthead - Full issue pdf
  2. Guest Editorial
  3. Outer Limits: Pushing the Extremities
  4. Contents
  5. Officer’s Column
  6. Secretary General’s Column
  7. Features
  8. The Three-letter Element Symbols:
  9. Procedures for the Naming of a New Element
  10. The Chemical Structure Association Trust
  11. IUPAC Wire
  12. Discovery and Assignment of Elements with Atomic Numbers 113, 115, 117 and 118
  13. Open Data in a Big Data World
  14. UN Secretary General Appoints ICSU Executive Director to Special Advisory Group on the SDGs
  15. Project Place
  16. Company Associates Reengineering Project
  17. Postgraduate Course in Polymer Science, Prague, Czech Republic
  18. Critically Evaluated ESR (EPR) Spectra of Important Polymerization-related Radicals
  19. Which Elements Belong in Group 3 of the Periodic Table?
  20. Making an imPACt
  21. Discovery of the elements with atomic numbers Z = 113, 115 and 117 (IUPAC Technical Report)
  22. Discovery of the element with atomic number Z = 118 completing the 7th row of the periodic table (IUPAC Technical Report)
  23. Glossary of terms used in computational drug design, part II (IUPAC Recommendations)
  24. Standard electrode potentials involving radicals in aqueous solution: inorganic radicals (IUPAC Technical Report)
  25. Maritime pollutants in shipping and commercial European ports based on relevant physical and biogeochemical environmental parameters (IUPAC Technical Report)
  26. Latest Updates from PAC Conferences & More—Brief
  27. IUPAC Provisional Recommendations
  28. Glossary of Terms Used in Developmental and Reproductive Toxicology
  29. How to Name Atoms in Phosphates, Polyphosphates, their Analogues, and Transition State Analogues for Enzyme-catalysed Phosphoryl Transfer Reactions
  30. Comprehensive Definition of Oxidation State
  31. Stamps International
  32. Berzelius and the Chemical Alphabet
  33. Conference Call
  34. Latin American Pesticide Residue Workshop—Food and Environment
  35. Ecological Risk Assessment
  36. Where 2B & Y
  37. New Chemistries for Phytomedicines and Crop Protection Chemicals
  38. Function Through Disorder: Intrinsically Disordered Proteins in Biology and Medicine
  39. Phosphorus Chemistry
  40. Self-assembly in the World of Polymers
  41. Solubility Phenomena
  42. Blood-Biomaterial Interactions
  43. CODATA-RDA School of Research Data Science
  44. 28th National [Turkish] Chemistry Congress with International Participation
  45. The Power of Norms
  46. Selenium Research (Se2017)
  47. Mark Your Calendar
Sign up now to receive a 20% welcome discount
Institutional Access
How does access work?
Have an idea on how to improve our website?
Please write us.
© 2025 De Gruyter Brill
Downloaded on 15.9.2025 from https://www.degruyterbrill.com/document/doi/10.1515/ci-2016-0221/html
Scroll to top button