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An atom is made of protons and neutrons which make up the nucleus and electrons that are around the nucleus. Although almost all the mass of an atom is in the nucleus, most of the space that the atom takes up is occupied by the electrons.
In very simple terms, the electrons are in orbits around the nucleus so most of the volume of the atom is empty space within the volume that the electrons occupy. The behaviour of the electrons is often assumed to be orbits but their actual positions are not that simple.

As a final note, all atoms contain neutrons with the exception of hydrogen which can exist as one proton and one electron.
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