An atomic-scale understanding of gas adsorption mechanisms on metal-porphyrins or metal-phthalocyanines is essential for their practical application in biological processes, gas sensing, and catalysis. Intensive research efforts have been devoted to the study of coordinative bonding with relatively active small molecules such as CO, NO, NH3, O2, and H2. However, the binding of single nitrogen atoms has never been addressed, which is both of fundamental interest and indeed essential for revealing the elementary chemical binding mechanism in nitrogen reduction processes. Here, we present a simple model system to investigate, at the single-molecule level, the binding of activated nitrogen species on the single Mn atom contained within the manganese phthalocyanine (MnPc) molecule supported on an inert graphite surface. Through the combination of in situ low-temperature scanning tunneling microscopy, scanning tunneling spectroscopy, ultraviolet photoelectron spectroscopy, X-ray photoelectron spectroscopy, and density functional theory calculations, the active site and the binding configuration between the activated nitrogen species (neutral nitrogen atom) and the Mn center of MnPc are investigated at the atomic scale.