In coulombs law, r is the distance between the charges. In theory these are point charges but what you are using in the lab is not a point charge but a sphere in this case what we do we assume that all the charge is concentrated at the center because of the symmetry (As an sphere i symmetric about its center) hence we take the distance between the centers.
There's another thing that the distance between the centers should be large in comparison of radius of the sphere.
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