  Qubits made from superconducting materials are a mature platform for quantum
information science application such as quantum computing. However,
materials-based losses are now a limiting factor in reaching the coherence
times needed for applications. In particular, knowledge of the atomistic
structure and properties of the circuit materials is needed to identify,
understand, and mitigate materials-based decoherence channels. In this work we
characterize the atomic structure of the native oxide film formed on Nb
resonators by comparing fluctuation electron microscopy experiments to density
functional theory calculations, finding that an amorphous layer consistent with
an Nb$_2$O$_5$ stoichiometry. Comparing X-ray absorption measurements at the
Oxygen K edge with first-principles calculations, we find evidence of d-type
magnetic impurities in our sample, known to cause impedance in proximal
superconductors. This work identifies the structural and chemical composition
of the oxide layer grown on Nb superconductors, and shows that soft X-ray
absorption can fingerprint magnetic impurities in these superconducting
systems.
