Abstract

Location and Volume of the Active Site of Chymotrypsin

P. V. Kostetsky

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia; fax: (495) 335-7103; E-mail: artem1@ibch.ru

Received February 17, 2006; Revision received September 1, 2006
The active site of chymotrypsin molecule (approximated by a sphere with radius of 20 Å) was taken as the largest cavity on the enzyme surface. The volume inside the approximating sphere is sufficient for placement of 95% of non-hydrogen atoms of the enzyme. The active site cavity is localized in a spherical sector with solid angle of 80° whose axis passes through the CB-atom of the Ser195 residue. The volume of the active site cavity is about 2700 Å³ (8% of the volume of the approximating sphere) as computed by the Monte-Carlo method from known X-ray data. The size and shape of the active site cavity is sufficient for entrance of significantly large fragments (more than 60 non-hydrogen atoms) of the substrate molecule. At the active site cavity bottom, there is a narrow compartment adjacent to an oxy-anion hollow and accessible to water but not to substrate molecules. The water molecules inside this narrow compartment can take part in heat exchange with the external medium during different steps of the enzymatic process.
KEY WORDS: approximating sphere, oxy-anion hollow, heat exchange
DOI: 10.1134/S0006297907040050