Abstract The chemical species of bridge oxygen (WB) in active site of urease was examined in terms of a magnetic interaction between Ni(II) ions. The effective exchange integrals ( J ab) values between Ni(II) ions were calculated by using three candidates of WB, i.e., H 2O, OH − and O 2−. The unrestricted hybrid density functional theory (UHDFT) calculations were carried out using the smallest models and realistic models. In the case of the smallest models, the experimental J ab value (−6.3 cm −1) was a middle value of WB = H 2O (−2.6 cm −1) and WB = OH − (−11.4 cm −1), while we could not obtain appropriate electronic structure using O 2−-bridge model. The J ab became −16.7 cm −1 by using more realistic OH −-bridge model, while one spin density on Ni2 ion was delocalized to Asp360 in case of H 2O-bridge model. Natural orbital analyses revealed that the magnetic orbital through Lys-bridge delocalized to Asp360 and it seemed to associate with the spin transfer. From the results, OH −-bridge seemed to be the most possible candidate for the structure of active site in urease.