We report sympathetic cooling of $^{113}$Cd$^+$ by laser-cooled $^{40}$Ca$^+$ in a linear Paul trap for microwave clocks. Long-term low-temperature confinement of $^{113}$Cd$^+$ ions was achieved. The temperature of these ions was measured at $90(10)$ mK, and the corresponding uncertainty arising from the second-order Doppler shifts was estimated to a level of $2times10^{-17}$. Up to $4.2times10^5$ Cd$^+$ ions were confined in the trap, and the confinement time constant was measured to be 84 hours. After three hours of confinement, there were still $10^5$ Cd$^+$ ions present, indicating that this Ca$^+$--Cd$^+$ dual ion system is surprisingly stable. The ac Stark shift was induced by the Ca$^+$ lasers and fluorescence, which was carefully estimated to an accuracy of $5.4(0.5)times10^{-17}$ using a high-accuracy textit{ab initio} approach. The Dick-effect-limited Allan deviation was also deduced because deadtimes were shorter. These results indicate that a microwave clock based on this sympathetic cooling scheme holds promise in providing ultra-high frequency accuracy and stability.
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