Figure 4

Internal cavities of KaiC and volume compaction on ATP hydrolysis. (A) Location of the cavity of the KaiC-ATP complex (PDB ID: 1U9I). Two subunits of KaiC (gray) and 6 ATP (gold) are depicted by ribbon and space-filling models, respectively. Mg⁺² ions and water molecules are depicted by cyan and red spheres, respectively. Catalytic residues for ATP hydrolysis are depicted by green stick models (i.e., E77, E78, E318, and E319). Cavities are depicted by dark-blue spheres, and were estimated using the MOLMOL program²⁵ with a 3.8-Å probe size. (B) Schematic of KaiC CI-CII domains of pre-hydrolysis and transition states. Three CI-CII domains are presented. Catalytic residues, ATP, water molecules, and cavities are depicted by green, yellow, red, and white circles, respectively.