Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + 2 H+.
ATP:4-(cytidine 5\'-diphospho)-2-C-methyl-D-erythritol 2-phosphotransferase activity