The direct conversion of methane to methanol using oxygen is a challenging but potentially rewarding pathway towards utilizing methane. By using a stepwise chemical looping approach, copper-exchanged zeolites can convert methane to methanol, but productivity is still too low for viable implementation. However, if the nature of the active site could be elucidated, that information could be used to design more effective catalysts. By employing anomalous X-ray powder diffraction with support from theory and other X-ray techniques, we have derived a quantitative and spatial description of the highly selective, active copper sites in zeolite omega (Cu-omega). This is the first comprehensive description of the structure of non-copper-oxo active species and will provide a pivotal model for future development for materials for methane to methanol conversion.