An atom has a nucleus at its centre. The nucleus is positively charged. Negatively charged electrons surround the nucleus.
An atom has no overall charge, because the positive charge of the nucleus is balanced by the negative charge of the electrons.
The radius of the nucleus is much smaller than the radius of the atom, thousands of times smaller, so most of the atom is empty space. Almost all of the mass of the atom is in the nucleus, because the electrons have a very small mass.