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Figure 5
Model DFT structures derived from the crystallographic data for nitrite binding at the T2Cu site. Asp98 (AspCAT) and His255 (HisCAT) are assumed to be protonated and are linked by hydrogen bonds to the bridging water molecule, W1. W2, which is the closest water to the T2Cu, is part of the highly conserved water network or `proton tube' (not shown here) linking the T1Cu and T2Cu sites to bulk solvent; this is a suggested route for proton delivery during catalysis. The hydrogen-bonding network is indicated by dashed lines, with bond lengths shown in Å. In the T2Cu(II) state (a), nitrite was found to relax to the top-hat orientation starting from either the top-hat or side-on crystal structure geometries, indicating that the side-on orientation is not stable in the T2Cu(II) state. In the T2Cu(I) state, the preferred orientation of nitrite after optimization depends on its starting geometry, indicating the presence of a barrier between the top-hat and side-on binding modes. Starting from the top-hat orientation, the relaxed coordination of nitrite at the T2Cu(I) state is an asymmetrical top-hat geometry (b); protonation and scission from this orientation are likely to lead to an end-on bound NO at the T2Cu site. Alternatively, starting from the side-on orientation, geometry optimization results in a distorted side-on nitrite coordination (c) that is 7.5 kcal mol−1 more stable than the asymmetric top-hat orientation in (b). The binding geometry in (c) is poised for the formation of side-on NO binding, with the nitrite O1 and N atoms bound to the T2Cu at 2.14 and 2.08 Å, respectively, while the O2 atom of nitrite is 2.71 Å from the T2Cu and oriented towards the AspCAT side chain.

IUCrJ
Volume 5| Part 3| May 2018| Pages 283-292
ISSN: 2052-2525
https://doi.org/10.1107/S205225251800386X