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Does EDTA take $\ce{Mg^{2+}}$ and $\ce{Mn^{2+}}$ out of solution, so that it can be removed by a filter? Or does it just take it out of any chemical reactions going on in the solution?

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No- still too small for normal filters. Those ions are in water complexes anyway. It doesn't stop (prevent) chemical reactions rather alter the thermodynamics. EDTA and other organic complexes are the common way to allow animals to absorb ions that would otherwise tend to form oxides when swallowed so its biologically (chemically) available.

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