An atom does not have more mass than its nucleus. In fact, the vast majority of an atom's mass is concentrated in its nucleus. The nucleus is the central part of an atom that contains protons and neutrons, which are collectively known as nucleons. Protons have a positive charge, and neutrons are neutral. Electrons, which are negatively charged particles, orbit the nucleus in regions known as electron shells or energy levels.
The mass of an electron is extremely small compared to the mass of a proton or neutron. Consequently, the combined mass of all the electrons in an atom is negligible compared to the mass of the nucleus. Therefore, most of the mass of an atom is concentrated in its nucleus.
However, when you measure the mass of an atom, it appears slightly greater than the sum of the masses of its individual protons and neutrons. This phenomenon is due to the binding energy that holds the nucleus together. According to Einstein's mass-energy equivalence (E=mc²), the energy associated with the binding of the nucleus contributes to the mass of the atom. This is known as the mass defect.
In summary, the nucleus of an atom contains the majority of its mass, while the electrons contribute only a tiny fraction. The apparent difference in mass arises from the binding energy within the nucleus.