Calculated membrane binding modes for PX domains of P40phoxwith lipid ligand PI(3)P (A) and P47phoxwith lipid ligand PI(3,4)P
(B). The backbone of PX domains and the specific lipid ligands are shown in ribbon and stick model, respectively. Residues identified as penetrating to the membrane in mutagenesis and binding experiments are colored red. Cationic residues involved in ligand binding and membrane interactions are colored blue. Hydrocarbon core boundary at the cytoplasmic side is indicated by blue dots. The layer of lipid phosphates ("P") is shown by gold dots (at 5 Å outside the hydrocarbon boundary). The center of membrane is indicated by grey dots (at 15 Å inside the boundary).