Photons are energy.
When an electron falls from a high energy level to a lower one the energy is released as a photon.
The atom doesn't contain a photon as such.
Atom as a whole dont't emit photons. Photon emission occurs when electron jumps from higher to lower energy level. Photon can also be produced by exciting the nucleus (remember internal conversion)...however in both the cases electrons are responsible for photon emission. Also when you deflect or make electron to accelerate in magnetic field...you can get photons.