Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement
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ORIGINAL PAPER
Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement Lili Cao1 · Octav Caldararu1 · Ulf Ryde1 Received: 15 May 2020 / Accepted: 14 August 2020 © The Author(s) 2020
Abstract Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ2 sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or N H2, i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum–mechanical calculations. This allows us to test various interpretations of the structure, employing quantum–mechanical calculations to predict the ideal structure and to use crystallographic measures like the real-space Z-score and electron-density difference maps to decide which structure fits the crystallographic raw data best. We show that the structure contains an O H−-bound state, rather than an N2-derived reaction intermediate. Moreover, the structure shows dual conformations in the active site with ~ 14% undissociated S2B ligand, but the storage site seems to be fully occupied, weakening the suggestion that it represents a storage site for the dissociated ligand. Graphic abstract
Keywords Nitrogenase · QM/MM · S2B dissociation · Nitrogen fixation · Quantum refinement
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00775-020-01813-z) contains supplementary material, which is available to authorized users. * Ulf Ryde [email protected] 1
Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00 Lund, Sweden
The atmosphere of Earth contains 78% N2, but nitrogen is still a limiting element for most plant life. The reason for this is that the triple bond in N2 is very strong, making N2 highly inert [1, 2]. In 1909, Fritz Haber designed a procedure to form ammonia from N2 and H2, employing high temperature and pressure. It was adapted for industrial use by Carl Bosch at BASF and is today known as
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the Haber–Bosch process. It is currently one of the most important industrial processes, consuming 1–2% of the world’s total energy supplies and it is a main reason for the human population explosion during the twentieth century, by providing abundant access to artificial fertilisers [3, 4]. In nature, a single enzyme, nitrogenase (EC 1.18/19.6.1), can convert N 2 to ammonia at ambient pressure and temperature [1, 5, 6]. It is found in a few bacteria and archaea, but many higher plants, e.g. legumes, rice and alder, live in symbiosis with such organisms, obtaining bio-available nitrogen in exchange for carbohydrates. The nitrogenase re
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