Open AccessProtonation and geometry of histidine rings
Author(s) -
Malinska Maura,
Dauter Miroslawa,
Kowiel Marcin,
Jaskolski Mariusz,
Dauter Zbigniew
Publication year - 2015
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s1399004715007816
Subject(s) - protonation , histidine , geometry , chemistry , crystallography , physics , mathematics , biochemistry , organic chemistry , amino acid , ion
The presence of H atoms connected to either or both of the two N atoms of the imidazole moiety in a histidine residue affects the geometry of the five‐membered ring. Analysis of the imidazole moieties found in histidine residues of atomic resolution protein crystal structures in the Protein Data Bank (PDB), and in small‐molecule structures retrieved from the Cambridge Structural Database (CSD), identified characteristic patterns of bond lengths and angles related to the protonation state of the imidazole moiety. Using discriminant analysis, two functions could be defined, corresponding to linear combinations of the four most sensitive stereochemical parameters, two bond lengths (ND1–CE1 and CE1–NE2) and two endocyclic angles (–ND1– and –NE2–), that uniquely identify the protonation states of all imidazole moieties in the CSD and can be used to predict which N atom(s) of the histidine side chains in protein structures are protonated. Updated geometrical restraint target values are proposed for differently protonated histidine side chains for use in macromolecular refinement.