Fig. 3: Structure of binding sites for ions and water.
From: Structural basis of vilazodone dual binding mode to the serotonin transporter
a Left: Side view of SERT showing the binding sites for Na1 (magenta sphere) and Cl (yellow sphere). The side chains forming the sites are shown (purple sticks). The EM density for ions and N101 are shown as mesh. The EM density of N101 is shown as a reference level corresponding to the density of SERT. Vilazodone is partly shown (red sticks). Right: Zoomed-in view showing the distances of coordinating residues to bound Cl as dashed lines. b Left: Side view of SERT showing Na1 and Na2 with the EM density as mesh. Resolved water molecules with EM density (mesh) and interacting residues are shown. Vilazodone is in red sticks. Right: Zoomed-in view showing the distances of coordinating residues to bound Na1 and Na2 as dashed lines. c Side view of SERT showing the hydrogen bonding network between the water molecules and Y95, D98, and F335. Hydrogen bonds (cyan dashed lines), Na1 and Na2, chloride, and vilazodone are shown.
