The HNH and RuvC domains are the nuclease domains responsible for cleavage. A lot of Lys, His, Asp, and Glu residues are responsible for binding Mg2+ and facilitating phopshodiester hydrolysis

@@thrax4939 Nerd

Cas9 is a nuclease(it can cut DNA or RNA strand)enzyme which is combined with a tracerRNA(which helps to bind to your target sequence ). This cas9 can cut because it has two domain( area) called 1.HNH and 2. RuvC-like domain.When cas9 binds to a target DNA sequence, its HNH part binds to the strand of the DNA that is complimentary to the tracerRNA, while RuvC-like domain binds to the non-complimentary strand. These two domains will cut both the strands of your target DNA.