The discovery of topological superconductivity in doped Bi$_2$Se$_3$ made this class of materials highly important for the field of condensed matter physics. However, the structural origin of the superconducting state remained elusive, despite being investigated intensively in recent years. We use scanning tunneling microscopy and the normal incidence x-ray standing wave (NIXSW) technique in order to determine the vertical position of the dopants -- one of the key parameters for understanding topological superconductivity in this material -- for the case of Sr$_{x}$Bi$_2$Se$_3$. In a novel approach we analyze the NIXSW data in consideration of the inelastic mean free path of the photoemitted electrons, which allows us to distinguish between symmetry equivalent sites. We find that Sr-atoms are not situated inside the van der Waals gap between the Bi$_2$Se$_3$ quintuple layers but rather in the quintuple layer close to the outer Se planes.
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