Employing first-principles density functional theory based calculations we investigated the change in electronic structure of CaCu3B4O12 compounds as one moves from 3d (Co) to 4d (Rh) to 5d (Ir) element at B site. Our study sheds light on valences of Cu and B ions as one moves from 3d to 4d to 5d based compounds. The valence of Cu in Co and Rh compound turn out to be that of less known 3+ state, while that in Ir compound turn out to be commonly known 2+ state. Our first-principles study provide microscopic understanding of these different valences of Cu, in terms of changes in the mixing of Cu x (2) - y (2) and B-a (1g) states, driven by changes in the crystal field and spin splitting. The stronger crystal field splitting for 4d and 5d elements compared to 3d at B site drive the low-spin state at Rh and Ir site as opposed to intermediate spin in case of Co.