Protein　kinase　CK2　(casein　kinase　2)　is　a　multifunctional　serine/threonine　kinase　that　is　involved　in　a　broad　range　of　physiological　events.　The　decreased　affinity　of　Emodin　binding　to　human　CK2　alpha　resulting　from　single-point　mutation　of　Val66　to　Ala　(V66A)　has　been　demonstrated　by　experimental　mutagenesis.　Molecular　dynamics　(MD)　simulations　and　energy　analysis　were　performed　on　wild　type　(WT)　and　V66A　mutant　CK2　alpha-Emodin　complexes　to　investigate　the　subtle　influences　of　amino　acid　replacement　on　the　structure　of　the　complex.　The　structure　of　CK2　alpha　and　the　orientation　of　Emodin　undergo　changes　to　different　degrees　in　V66A　mutant.　The　affected　positions　in　CK2　alpha　are　mainly　distributed　over　the　glycine-rich　loop　(G-loop),　the　alpha-helix　and　the　loop　located　at　the　portion　between　G-loop　and　alpha-helix　(C-loop).　Based　on　the　coupling　among　these　segments,　an　allosteric　mechanism　among　the　C-loop,　the　G-loop　and　the　deviated　Emodin　is　proposed.　Additionally,　an　estimated　energy　calculation　and　residue-based　energy　decomposition　also　indicate　the　lower　instability　of　V66A　mutant　in　contrast　to　WT,　as　well　as　the　unfavorable　energetic　influences　on　critical　residue　contributions.