Figure 3

Shape and surface features of the ATP-binding pocket of the YycG HATPase_c domain in S. epidermidis. (A). View from the front of the pocket of the HATPase_c domain. (B) View from the top of the pocket of the HATPase_c domain. To display the bottom of the pocket clearly, some residues which cover the top of the pocket were taken off from the surface. The ATP binding pocket is fairly large and deep. Two cavities joined by a gorge-like channel construct the whole binding pocket. The inner small cavity of the pocket is hydrophobic, composed of residues Phe498, Val501, Phe56, Ile53, and the adenine ring of natural ligand ATP may interact with this area just as in the NMR structure of EnvZ[24]. The space compressed by Asn503 and Lys542 in the middle of the pocket form the narrow channel. The outer large cavity of pocket divides into two parts (I and II) in terms of its surface property. Area I composed of residues Phe46, Thr483, Ile484, Phe485, Met493, and Leu598, exhibits hydrophobic character; Area II locates near entrance of the binding pocket and show hydrophilic character. Schematic diagrams were made with the MOLCAD program in Sybyl (see Methods).