Fig. 5. Effects of the presence or absence of Ca²⁺ ion in XacGH43_1 active site.

a Representation of the −1 subsite in the presence of Ca²⁺ in the metal-binding site. b Snapshot of the MD simulation in which the Ca²⁺ was initially replaced by a water molecule, followed by Na⁺ (from the solvent) entrance to the metal-binding site. Here the His288 adopts a different conformation (rotamer 2) and interacts with Asp30 (general base) and Asp30 interacts with the xylosyl H2. c A snapshot from the same simulation of b, with the Na⁺ being coordinated by His288. The interaction of Asp30-xylosyl H2 is maintained. Distances in a–c are represented in angstroms. d Distances between Asp150 O_δ2 and xylosyl H2 atoms during the production of the three MD independent simulations with Ca²⁺ (blue) or with water (spontaneously replaced by Na⁺ during the course of the simulation) (pink). Averages are shown as solid symbols and the SD with lighter colors. Data points are shown as empty symbols. e His288 dihedral angle distribution of the rotamers 1 and 2 during the MD simulation with Ca²⁺. f Same results in the MD simulation without Ca²⁺ (spontaneously replaced by Na⁺ during the course of the simulation). Source data are provided as a source data file.