Single metal atoms embedded in nitrogen-doped graphene (M–N–C) have emerged as a promising catalyst for a wide variety of reactions. In addition to the pyridinic site, there is another site responsible for the catalytic activity, but its structure is under debate. Here, we resolve its structure using first-principles calculations. Using Fe–N–C as a representative example, we systematically explore numerous possible structures and discover a new moiety with comparable energy to the pyridinic. This moiety features a hybrid coordination environment between pyridinic and porphyrinic and is located at the edge of graphene sheets or pores. We further calculate its X-ray absorption spectrum, catalytic thermodynamics for oxygen reduction reaction (ORR), and stability under ORR conditions, all of which support its existence. Lastly, we show that this site also exists in other M–N–C with different M elements. This study uncovers a new and important structure in M–N–C and paves a critical step toward site engineering for improved catalytic performance.