The interplay of the calcium concentration and the anatomical structure at the presynaptic zone of presynaptic boutons is an important challenge of the relationship of form and function in (computational) neuroscience. A simple model system to study such basic effects is the neuromuscular junction of the Drosophila larva (NMJ). At this synapse, specific structures can be found. Its presynaptic boutons are larger than usual vertebrate synapses, also they bear several presynaptic zones. Different anatomic structures can be found at these zones. In part, they incorporate a so-called T-Bar, which, at the first glance, reminds us of the letter "T" in 2D view, and a table with one leg in 3D view. Calcium influx is triggered by action potentials, and the release probability of vesicles depends on the calcium concentration close to the vesicular release site. Assuming that the T-bar might cause calcium concentration enhancement and thus triggers an enhanced release probability, the T-bar indirectly would enhance as well the neurotransmitter exocytosis. This study evaluates the influence of the T-bar anatomy upon the calcium concentration in a quantitative manner by means of full 3D computations of a partial differential equation (PDE) model of calcium influx, calcium concentration and dynamics at the presynaptic zone. Comparing the cases of the calcium concentrations for the scenario of a synaptic zone harboring a T-bar geometry with another one without T-bar by means of evaluating the calcium concentrations close to the active zones (AZ), this study demonstrates a major influence of the T-bar structure upon the presynaptic calcium concentration close to the AZ. The computations allow to determine quantitatively the influence of the anatomical structure of the T-bar upon the calcium concentration, and thus allows to relate the form and function of the T-bar with the neurotransmitter release probability. In fact, this purely theoretical study allows to give an answer to one of the major questions discussed in the experimental study of “Wichmann and Sigrist, Journal of Neurogenetics 2010”, which asked if the T-bar anatomical structure has a biophysical impact.