As you can see the atom consists not only of the nucleus and electron but also of "empty space is the space empty or is their something else?
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2$\begingroup$ There is a question and answer on Physics.SE physics.stackexchange.com/questions/7615/… $\endgroup$ – user15489 Apr 19 '15 at 10:23
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It is not necessarily empty space.
For example the flux of neutrinos on Earth is about $3 \times 10^{12}/cm^2/s$. At a given moment, a neutrino may or may not be within the atom or even within the nucleus of the atom. Similarly, other particles may be present within an atom at a given time.
Also, an electron may be inside the nucleus in accordance with the Fermi Contact Interaction. So if you have a hydrogen atom, having only one electron, and the electron is inside the nucleus at a given moment, there will be no "between" for there to be space, empty or not.
