Substrate binding
Substrate binding sites or catalytic sites of multi-domain proteins are often situated within a cleft between two domains. Relative, rigid body movements between the two adjacent domains allows an induced-fit binding of the substrate and the creation of a catalytic environment that is isolated from the solvent.
A few examples:
3. calmodulin, free and bound to a helical peptide
Gerstein, Lesk and Chothia describe many more examples of domain movements involved in induced fit binding.
Reference
back to roles of protein domains