Figure 4

Schematic diagram of Emodin binding models against HpFabZ. The electrostatic surface of the active tunnel is rendered by a color ramp from red to blue. Emodin and surrounding critical residues are shown as sticks; water molecules that interact with Emodin are shown as red sphere. Hydrogen bonds are shown as yellow dashes. Emodin is colored wheat, and residues are colored in yellow, magenta, blue and orange for monomers A, B, C and D, respectively. The diagram was produced by the program Pymol. (A) Binding model A of Emodin around the entrance of tunnel B. Emodin binds to the entrance of tunnel B linearly through hydrophobic interactions, and is stacked between residues Tyr100 and Pro112'. (B) The interactions between Emodin and residues nearby (as well as some water molecules) in model A are indicated. Ring A of Emodin is stacked between Tyr100 and Pro112' forming a sandwich structure. 3'-methyl of ring A and C forms hydrophobic interactions with residues near the tunnel entrance. In addition, 6'-hydroxyl of ring C interacts with water molecule W466 through hydrogen bond. (C) Binding model B of Emodin near the catalytic site of tunnel C. Emodin extents to the bottom of the tunnel and is located in the hydrophobic pocket. (D) The interactions between Emodin and residues nearby (as well as some water molecules) in model B are indicated. The whole molecule of Emodin hydrophobic interacts with residues near by as well as hydrogen bonded interacts with waters W12 and W402 through its 6'-hydroxyl of ring C.