Carboxylate binding modes in zinc proteins : A theoretical study
Ryde, Ulf LU
(1999)
In Biophysical Journal
77(5).
p.2777-2787
- Abstract
The relative energies of different coordination modes (bidentate, monodentate, syn, and anti) of a carboxylate group bound to a zinc ion have been studied by the density functional method B3LYP with large basis sets on realistic models of the active site of several zinc proteins. In positively charged four-coordinate complexes, the mono- and bidentate coordination modes have almost the same energy (within 10 kJ/mol). However, if there are negatively charged ligands other than the carboxylate group, the monodentate binding mode is favored. In general, the energy difference between monodentate and bidentate coordination is small, 4-24 kJ/mol, and it is determined more by hydrogen-bond interactions with other ligands or second- sphere... (More)
The relative energies of different coordination modes (bidentate, monodentate, syn, and anti) of a carboxylate group bound to a zinc ion have been studied by the density functional method B3LYP with large basis sets on realistic models of the active site of several zinc proteins. In positively charged four-coordinate complexes, the mono- and bidentate coordination modes have almost the same energy (within 10 kJ/mol). However, if there are negatively charged ligands other than the carboxylate group, the monodentate binding mode is favored. In general, the energy difference between monodentate and bidentate coordination is small, 4-24 kJ/mol, and it is determined more by hydrogen-bond interactions with other ligands or second- sphere groups than by the zinc-carboxylate interaction. Similarly, the activation energy for the conversion between the two coordination modes is small, ~6 kJ/mol, indicating a very flat Zn-O potential surface. The energy difference between syn and anti binding modes of the monodentate carboxylate group is larger, 70-100 kJ/mol, but this figure again strongly depends on interactions with second-sphere molecules. Our results also indicate that the pK(a) of the zinc-bound water ligand in carboxypeptidase and thermolysin is 8-9.
(Less)
- author
- Ryde, Ulf
LU
- organization
- publishing date
- 1999-11
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Biophysical Journal
- volume
- 77
- issue
- 5
- pages
- 11 pages
- publisher
- Cell Press
- external identifiers
-
- pmid:10545376
- scopus:0032708644
- ISSN
- 0006-3495
- DOI
- 10.1016/S0006-3495(99)77110-9
- language
- English
- LU publication?
- yes
- id
- 82b03c52-b954-4c69-970f-15c846c118dd
- date added to LUP
- 2017-02-04 11:41:23
- date last changed
- 2025-04-14 14:16:39
@article{82b03c52-b954-4c69-970f-15c846c118dd,
abstract = {{<p>The relative energies of different coordination modes (bidentate, monodentate, syn, and anti) of a carboxylate group bound to a zinc ion have been studied by the density functional method B3LYP with large basis sets on realistic models of the active site of several zinc proteins. In positively charged four-coordinate complexes, the mono- and bidentate coordination modes have almost the same energy (within 10 kJ/mol). However, if there are negatively charged ligands other than the carboxylate group, the monodentate binding mode is favored. In general, the energy difference between monodentate and bidentate coordination is small, 4-24 kJ/mol, and it is determined more by hydrogen-bond interactions with other ligands or second- sphere groups than by the zinc-carboxylate interaction. Similarly, the activation energy for the conversion between the two coordination modes is small, ~6 kJ/mol, indicating a very flat Zn-O potential surface. The energy difference between syn and anti binding modes of the monodentate carboxylate group is larger, 70-100 kJ/mol, but this figure again strongly depends on interactions with second-sphere molecules. Our results also indicate that the pK(a) of the zinc-bound water ligand in carboxypeptidase and thermolysin is 8-9.</p>}},
author = {{Ryde, Ulf}},
issn = {{0006-3495}},
language = {{eng}},
number = {{5}},
pages = {{2777--2787}},
publisher = {{Cell Press}},
series = {{Biophysical Journal}},
title = {{Carboxylate binding modes in zinc proteins : A theoretical study}},
url = {{http://dx.doi.org/10.1016/S0006-3495(99)77110-9}},
doi = {{10.1016/S0006-3495(99)77110-9}},
volume = {{77}},
year = {{1999}},
}