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Considerable scientific research supports the idea that urine citrate reduces crystallization of calcium kidney stone salts. The research includes two prospective double blind controlled kidney stone prevention trials. Citrate binds calcium, reducing the fraction free to bind with oxalate or phosphate. Citrate inhibits formation and growth of calcium stone forming crystals. Almost certainly, brushite or octocalcium phosphate crystals help initiate calcium oxalate crystallization in urine, and citrate strongly inhibits that process.
Kidney cells control how much citrate is in the urine. Blood concentration is high enough that large amounts of citrate are filtered, but much of the filtered citrate is reabsorbed back into kidney proximal tubule cells that metabolize it for energy. The reabsorption of filtered citrate is controlled strongly by the acid load diet and metabolism impose on the body. When acid load is high, kidneys reabsorb a higher fraction of citrate leaving less in the urine. With alkali loads, the opposite.
This makes sense because citrate is metabolized as citric acid, so it takes up a proton – essentially produces new blood bicarbonate – as it is used by cells.