In the microscopic world, multipartite entanglement has been achieved with various types of nanometer-sized two-level systems such as trapped ions, atoms and photons. On the macroscopic scale ranging from micrometers to millimeters, recent experiments have demonstrated bipartite and tripartite entanglement for electronic quantum circuits with superconducting Josephson junctions. It remains challenging to bridge these largely different length scales by constructing hybrid quantum systems. Doing so may allow us to manipulate the entanglement of individual microscopic objects separated by macroscopically large distances in a quantum circuit. Here we report on the experimental demonstration of induced coherent interaction between two intrinsic two-level states (TLSs) formed by atomic-scale defects in a solid via a superconducting phase qubit. The tunable superconducting circuit serves as a shuttle communicating quantum information between the two microscopic TLSs.We present a detailed comparison between experiment and theory and find excellent agreement over a wide range of parameters.We then use the theoretical model to study the creation and movement of entanglement between the three components of the quantum system.