We measure the impact of nonvanishing boundary localised terms on $Delta B=2$ transitions in five-dimensional Universal Extra Dimensional scenario where masses and coupling strengths of several interactions of Kaluza-Klein modes are significantly modified with respect to the minimal counterpart. In such scenario we estimate the Kaluza-Klein contributions of quarks, gauge bosons and charged Higgs by evaluating the one-loop box diagrams that are responsible for the $Delta B=2$ transitions. Using the loop function (obtained from one-loop box diagrams) we determine several important elements that are involved in Wolfenstein parametrisation. Moreover, with these elements we also study the geometrical shape of unitarity triangle. Besides, we compute the quantity $Delta M_s$ scaled by the corresponding Standard Model value. Outcomes of our theoretical predictions have been compared to the allowed ranges of the corresponding observables simultaneously. Our current analysis shows that, depending on the parameters in this scenario the lower limit on the inverse of the radius of compactification can reach to an appreciable large value ($approx 1.48$ TeV or even higher).
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