The calcium-calmodulin (CaM) dependent protein Kinase-II (CaMKII) regulates various cellular process and has been implicated in illness including schizophrenia, heart failure, arthritis, and even certain types of cancers. CaMKII subunits assemble to form a large dodecameric holoenzyme. The structure of a kinase subunit is organized into 3 domains, a catalytic domain, a regulatory domain, and an oligomerization domain. Each N-terminal catalytic domain harbors the kinase catalytic site, its ATP binding site, as well as the so-called ‘T-site’, thought to interact with the T286 autophosphorylation site in the regulatory domain. The T-site is responsible for mediating the interaction of the holoenzyme with other proteins, such as NMDA receptors, in response to activation. The catalytic domain is attached to an autoinhibitory regulatory domain that contains the T286 autophosphorylation site, and a CaM-binding site. In turn: the regulatory domain is itself tethered to a C-terminal oligomerization domain that organizes the enzyme into ring-shaped oligomers. We have previously shown in living cells using FRET analysis that catalytic domains form pairs in the intact auto-inhibited holoenzyme. In Hippocampal neurons, these pairs separate in response to calcium influx through NMDA-receptors, but it is not known if this is a direct response to CaM binding, or a down stream affect of kinase activation. Here using fluorescence polarization and fluctuation analysis (FPFA), a hybrid method that simultaneously measures homo-FRET and fluorescence correlation spectroscopy (FCS), we show that CaMKIINtide, a T-site ligand, disrupts catalytic domain pairing in the intact holoenzyme. This reaction is dose dependent but was only observed upon co-incubation with CaM to activate the enzyme. The holoenzyme can be activated without catalytic domain pair separation. We also show that T-site specific mutations at I205, stabilize catalytic domain pairing and counteract CaMKIINtide's ability to disrupt catalytic domain pairing.