Fig. 8
From: Structural basis of denuded glycan recognition by SPOR domains in bacterial cell division
Dynamic interactions that stabilize denuded PG (1) with SPOR-RlpA, as calculated by molecular-dynamics simulation. a The interactions of 1 with SPOR-RlpA are depicted per the energy-minimized X-ray complex. b The dynamics fluctuations in intermolecular interactions are shown as distances between protein and ligand atoms in the line-plots and box-plots (on the right) calculated for ten thousand sampled conformations of the 500 ns MD simulation. The boxes in the middle of the box plots show the middle 50% of the sampled distances, while the upper and lower lines of the box represent upper and lower 25% of the distances. The horizontal lines inside the box denote the median value. The dots at the end of the lines, if present, are outliers. For consistency in plotting the y-axis, the values in the range of 2–8 Å of the distances are plotted in all the figures. N276, A275: Distance between carboxylate oxygen* of NAM(3) and main-chain nitrogen atoms of residues N276 and A276 respectively. A273: Distance between 3-hydroxyl oxygen atom of NAG(2) and main-chain nitrogen atom of A273.A273-N: distance between main-chain oxygen atom of A273 with acetamide nitrogen atom of NAM(3). R302, R309, and R311: Distance between the oxygen* atom of the carboxylate group of NAM(1) with the nitrogen** atom of arginine residue. (Indicated by yellow broken line in the Fig. 6a).CH-pi: Distance between the centroid of the aromatic ring of F274 and centroid of three of the carbon atoms (C1, C3, and C5) of NAG(3). *Any of the two oxygen atoms of the carboxylate group with least distance to interacting nitrogen atom. **Any of the three nitrogen atoms of each arginine residues with least distance to interacting oxygen atom.
