Ca2+-Calmodulin-dependent protein kinase II (CaMKII) is an interpreter of Ca2+ signaling and has been shown to be a critical component of learning and memory. This dodecameric oligomer also functions in part as a scaffolding molecule, serving to promote the formation of higher order signaling complexes within synapses. We set to study the effect that divalent cations, known to be critically important in neuronal signaling, have on the structure and function CaMKII. First, we computed the electrostatic surface potential of the dodecameric complex as a means to predict possible binding sites for divalent cations. A discrete set of high probability binding sites were identified at the interface between catalytic and association domains of neighboring subunits, far from the Mg2+ binding sites required to coordinate ATP in the catalytic cleft. Next, we experimentally characterized the effects of divalent cations on CaMKII structure using fluorescence, light scattering and electron microscopy. We found that some, but not all, divalent ions including Zn2+ promote the reversible formation of self-assembled CaMKII fibers that can extend for several μm. When associated in fibers, CaMKII activity is compromised; however, Ca2+/CaM activation of the enzyme disassembles fibers and the loss of activity is reversed. Interestingly, fiber assembly does not interfere with the autophosphorylation of CaMKII at T286, an autoregulatory modification, which confers autonomous activity in monodisperse CaMKII. We compile our results with structural and mechanistic data from literature to propose a model of Zn2+-mediated CaMKII fiber formation, where Ca2+/CaM regulates fiber formation through allosteric modification of a divalent ion site identified in our electrostatic map.