Figure 5.

The position of arabinose in the active site of EcoRK (structure obtained through cluster analysis of 400-ns long MD trajectory). The semi-transparent surface represents the hydrophobic interface in the lid domain, formed by Ala98, Ile100 and Ile110.Residues 248–251 and 285–295 are hidden. Carbon atoms of arabinose are colored green, carbon atoms of residues Ala98, Ile100 and Ile110—orange, oxygen atoms—red, nitrogen atoms—blue. Yellow dashed lines represent polar contacts; other colors distances measured throughout the MD simulation and represented in Figure 4F,G. Visualization was performed in PyMOL 2.0 (Schrödinger, LLC).