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The process of coupling lysine to lysyl-tRNA in a mitochondrion, catalyzed by lysyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2\'- or the 3\'-hydroxyl group of the 3\'-adenosine residue of the tRNA. [GOC:mah, GOC:mcc]
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