ScdA is a Repair Iron Cluster (RIC) protein found in S. aureus, which is believed to resist iron-sulfur clusters damaged by nitrosative or oxidative stress, such as nitric oxide (NO) and hydrogen peroxide (H2O2). S. aureus is known to cause a variety of clinical diseases in humans, and treating them is difficult due to drug resistance. When S. aureus infects humans, macrophages release NO or H2O2 to attack its iron-sulfur clusters. At the same time, the high concentration of NO or H2O2 induces the expression of ScdA in S. aureus. Therefore, understanding the relationship between ScdA's function and structural changes could help us inhibit its function. Previous literature reports that ScdA is a homodimer protein with two iron atoms per monomer, but no experimental data have described its structure thus far. In our study, we used site-directed spin labeling and continuous-wave EPR spectroscopy (CW-EPR) to probe protein dynamics in different regions of ScdA. We also used double electron-electron resonance (DEER) spectroscopy to measure the distance between the two spin-label side-chains on the protein to reproduce its structure. Alpha-fold prediction shows that ScdA is divided into two regions, the N- and C-domains. Our CW-EPR experiment results indicate that the C-domain's dynamics are more rigid than the N-domain's. The DEER experiment also shows that the conformational dynamics between the C-domains of the homodimer are greater than between the N-domains. In the mutation experiment, we identified a critical residue at the interface between the monomer units. Our study revealed molecular details of the ScdA dimer's structural conformations. Overall, our study provides experimental data to describe the structure of ScdA and its dynamics in different protein regions. These findings can aid in understanding the relationship between ScdA's function and structural changes and ultimately help in developing strategies to inhibit its function.