as one unit of CK2 defined as the amount of required to catalyze the transfer of 1 pmol of phosphate to CK2 Peptide Substrate, RRRADDSDDDDD (100 µM), in 1 minute at 30°C. But I don't know the unit of CK-2 I have I know its Conc. in mg/ml. please tell me how much CK-2 (in mg) will require to phosphorylate 1mg of protein having three phosphorylation sites in it
First, you have to know how many units of CK2 you have per volume of your protein. This can be done by testing the activity of the enzyme using the substrate peptide you mention. Your concentration of protein does not tell you if, for instance, only 70% of the molecules are active, so you have to run a proper kinase assay. This number will tell you how many sites are phosphorylated (at that concentration of peptide) per time unit.
Secondly, assuming the phosphorylation of the tree sites of the protein is not cooperative, your value should be roughly three times smaller (having three independent sites means you need to process the protein three times with CK2 to have the three sites phosphorylates). However, this value is very likely a rough approximation and pre-phosphorylated sites favor the processing to nearby phospho-acceptors with CK2. If you need your protein to be completely phosphorylated you can run a time-course experiment and check your samples via "upshift" estimation from SDS-PAGE or similar quantitative techniques as intact-MassSpectrometry.
Another caveat... your rate is dependent on the concentration of the substrates (ATP and substrate) concentration. In order to use the value calculated from the first point above and apply it to the second point, your concentration of peptide for the activity assays would need to be the same as in the protein-phosphorylation. And again, the activity might be affected by the "sterical" availability of sites in the protein, whereas the peptide is inherently less hindered.
Moreover, all assumptions made on the peptides, are valid irrespective of the form of CK2 you work with (alpha only or tetrameric alpha2-beta2). You should assess if your substrate is one that is better phosphorylated by one form or the other. You might find more infos in the review by Meggio and Pinna (2003) - http://www.ncbi.nlm.nih.gov/pubmed/12631575
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