Chemical and computer graphics studies on the topography of the ribonuclease A active site cleft. A model of the enzyme-pentanucleotide substrate complex.

The affinity labelling of bovine pancreatic ribonuclease A with 6-chloropurine 5' ribonucleotide allowed us to postulate the existence of a new phosphate-binding subsite, P2, adjacent to the main purine-binding subsite. The study of this reaction in greater detail together with the study of a complex of the enzyme with the pentanucleotide pApUpApApG by means of model building and computer graphics indicate that at least five phosphate groups of the RNA molecule can interact with five positive regions of the enzyme. In each one a lysine residue is present: Lys-104, -66, -41, -7 and -37 appear sequentially in the 5'----3' direction. The distance between each lysine is 0.7-0.8 nm, the same distance as that found between the phosphate groups on the RNA molecule. The study also enabled many amino acid residues of the enzyme to be described as forming part of, or being near, the different binding subsites.