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Critical evaluation of a crystal structure of nitrogenase with bound N2 ligands

Bergmann, Justin LU ; Oksanen, Esko LU and Ryde, Ulf LU (2021) In Journal of Biological Inorganic Chemistry
Abstract

Recently, a 1.83 Å crystallographic structure of nitrogenase was suggested to show N2-derived ligands at three sites in the catalytic FeMo cluster, replacing the three μ2 bridging sulfide ligands (two in one subunit and the third in the other subunit) (Kang et al. in Science 368: 1381–1385, 2020). Naturally, such a structure is sensational, having strong bearings on the reaction mechanism of the enzyme. Therefore, it is highly important to ensure that the interpretation of the structure is correct. Here, we use standard crystallographic refinement and quantum refinement to evaluate the structure. We show that the original crystallographic raw data are strongly anisotropic, with a much lower resolution in certain... (More)

Recently, a 1.83 Å crystallographic structure of nitrogenase was suggested to show N2-derived ligands at three sites in the catalytic FeMo cluster, replacing the three μ2 bridging sulfide ligands (two in one subunit and the third in the other subunit) (Kang et al. in Science 368: 1381–1385, 2020). Naturally, such a structure is sensational, having strong bearings on the reaction mechanism of the enzyme. Therefore, it is highly important to ensure that the interpretation of the structure is correct. Here, we use standard crystallographic refinement and quantum refinement to evaluate the structure. We show that the original crystallographic raw data are strongly anisotropic, with a much lower resolution in certain directions than others. This, together with the questionable use of anisotropic B factors, give atoms an elongated shape, which may look like diatomic atoms. In terms of standard electron-density maps and real-space Z scores, a resting-state structure with no dissociated sulfide ligands fits the raw data better than the interpretation suggested by the crystallographers. The anomalous electron density at 7100 eV is weaker for the putative N2 ligands, but not lower than for several of the μ3 bridging sulfide ions and not lower than what can be expected from a statistical analysis of the densities. Therefore, we find no convincing evidence for any N2 binding to the FeMo cluster. Instead, a standard resting state without any dissociated ligands seems to be the most likely interpretation of the structure. Likewise, we find no support that the homocitrate ligand should show monodentate binding. Graphic abstract: [Figure not available: see fulltext.].

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author
; and
organization
publishing date
type
Contribution to journal
publication status
epub
subject
keywords
N binding, Nitrogenase, Quantum refinement, Reaction intermediates
in
Journal of Biological Inorganic Chemistry
publisher
Springer
external identifiers
  • scopus:85102713319
  • pmid:33713183
ISSN
0949-8257
DOI
10.1007/s00775-021-01858-8
language
English
LU publication?
yes
id
2d6f4ef9-7614-49f6-b27a-9e960bf54004
date added to LUP
2021-04-01 09:33:18
date last changed
2021-05-11 02:54:51
@article{2d6f4ef9-7614-49f6-b27a-9e960bf54004,
  abstract     = {<p>Recently, a 1.83 Å crystallographic structure of nitrogenase was suggested to show N<sub>2</sub>-derived ligands at three sites in the catalytic FeMo cluster, replacing the three μ<sub>2</sub> bridging sulfide ligands (two in one subunit and the third in the other subunit) (Kang et al. in Science 368: 1381–1385, 2020). Naturally, such a structure is sensational, having strong bearings on the reaction mechanism of the enzyme. Therefore, it is highly important to ensure that the interpretation of the structure is correct. Here, we use standard crystallographic refinement and quantum refinement to evaluate the structure. We show that the original crystallographic raw data are strongly anisotropic, with a much lower resolution in certain directions than others. This, together with the questionable use of anisotropic B factors, give atoms an elongated shape, which may look like diatomic atoms. In terms of standard electron-density maps and real-space Z scores, a resting-state structure with no dissociated sulfide ligands fits the raw data better than the interpretation suggested by the crystallographers. The anomalous electron density at 7100 eV is weaker for the putative N<sub>2</sub> ligands, but not lower than for several of the μ<sub>3</sub> bridging sulfide ions and not lower than what can be expected from a statistical analysis of the densities. Therefore, we find no convincing evidence for any N<sub>2</sub> binding to the FeMo cluster. Instead, a standard resting state without any dissociated ligands seems to be the most likely interpretation of the structure. Likewise, we find no support that the homocitrate ligand should show monodentate binding. Graphic abstract: [Figure not available: see fulltext.].</p>},
  author       = {Bergmann, Justin and Oksanen, Esko and Ryde, Ulf},
  issn         = {0949-8257},
  language     = {eng},
  publisher    = {Springer},
  series       = {Journal of Biological Inorganic Chemistry},
  title        = {Critical evaluation of a crystal structure of nitrogenase with bound N<sub>2</sub> ligands},
  url          = {http://dx.doi.org/10.1007/s00775-021-01858-8},
  doi          = {10.1007/s00775-021-01858-8},
  year         = {2021},
}