The water oxidation reaction, the most important reaction for hydrogen production and other sustainable chemistry, is efficiently catalyzed by the Mn4CaO5 cluster in biological photosystem II. However, synthetic Mn-based heterogeneous electrocatalysts exhibit inferior catalytic activity at neutral pH under mild conditions. Symmetry-broken Mn atoms and their cooperative mechanism through efficient oxidative charge accumulation in biological clusters are important lessons but synthesis strategies for heterogeneous electrocatalysts have not been successfully developed. Here, we report a crystallographically distorted Mn-oxide nanocatalyst, in which Ir atoms break the space group symmetry from I41/amd to P1. Tetrahedral Mn(II) in spinel is partially replaced by Ir, surprisingly resulting in an unprecedented crystal structure. We analyzed the distorted crystal structure of manganese oxide using TEM and investigated how the charge accumulation of Mn atoms is facilitated by the presence of a small amount of Ir.