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Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase

Bergmann, Justin (author)
Lund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH
Oksanen, Esko (author)
European Spallation Source ESS ERIC
Ryde, Ulf (author)
Lund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH
 (creator_code:org_t)
Elsevier BV, 2021
2021
English.
In: Journal of Inorganic Biochemistry. - : Elsevier BV. - 0162-0134. ; 219
  • Journal article (peer-reviewed)
Abstract Subject headings
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  • Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to plants (although the enzyme itself is strictly microbial). It has been studied extensively with both experimental and computational methods, but many details of the reaction mechanism are still unclear. X-ray crystallography is the main source of structural information for biomacromolecules, but it has problems to discern hydrogen atoms or to distinguish between elements with the same number of electrons. These problems can sometimes be alleviated by introducing quantum chemical calculations in the refinement, providing information about the ideal structure (in the same way as the empirical restraints used in standard crystallographic refinement) and comparing different interpretations of the structure with normal crystallographic and quantum mechanical quality measures. We have performed such quantum-refinement calculations to address two important issues for nitrogenase. First, we show that the bidentate ligand of the active-site FeV cluster in V‑nitrogenase is carbonate, rather than bicarbonate or nitrate. Second, we study the CO-inhibited structure of Mo‑nitrogenase. CO binds to a reduced and protonated state of the enzyme by replacing one of the sulfide ions (S2B) in the active-site FeMo cluster. We examined if it is possible to deduce from the crystal structure the location of the protons. Our results indicates that the crystal structure is best modelled as fully deprotonated.

Subject headings

NATURVETENSKAP  -- Kemi -- Oorganisk kemi (hsv//swe)
NATURAL SCIENCES  -- Chemical Sciences -- Inorganic Chemistry (hsv//eng)

Keyword

Carbonate
Nitrogenase
Protonation
Quantum refinement

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art (subject category)
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Bergmann, Justin
Oksanen, Esko
Ryde, Ulf
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NATURAL SCIENCES
NATURAL SCIENCES
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and Inorganic Chemis ...
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Journal of Inorg ...
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Lund University

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