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MeThe citrate molecule in urine is thought to protect against formation of calcium stones. This thought began as reasoning from chemistry, and culminated in clinical trials which substantiate the idea. As a result manufacturers produce citrate products for medicinal use, and doctors prescribe the medicine.

All this is a wonderful success story, a kind of perfection of the paradigm of translational science: From science to a treatment for patients that reduces illness from kidney stone disease.

But what, exactly, is the science? Can scientists not enjoy the story of such a success, physicians derive from it a deeper understanding of the drug they so regularly dispense and patients the comfort that a perfected knowledge support the rightness of their prescribed treatment?


The Molecule

As usual in such diagrams the carbon atoms are simply angles or kinks. Reading from left to right, there is a carbon atom bound (the solid lines) to two oxygen atoms (‘O’), one with a single and the other with a double bond. These bonds represent sharing of electrons by the atoms.
The single bonded oxygen has an extra electron in its outer shell, so it carries a negative charge (-). Calcium is an atom with two positive charges, so the idea of calcium and citrate binding to each other comes naturally as one thinks about opposites attracting one another.

Next in line is another carbon atom; the kink means the carbon is linked to the carbons on its left and right and to two hydrogen atoms. The hydrogen atoms are necessary because every carbon atom makes four bonds.

After that, is the third carbon which is very occupied. It has an oxygen which is itself bound to a hydrogen – a hydroxyl molecule, really 2/3 of a water molecule – and another carbon bound to two oxygens, one of which has a negative charge. To the right of this busy carbon the molecule repeats itself as in a mirror.

How beautiful nature is, how powerful its symmetries and suggestive its forms!

It is as though some great sculptress were taken with an image of perfection that a string of carbons might take the perfect form to mate with calcium, tiny in comparison, and doubly charged positive.

But how? How would the mating occur? If you do not look down, could you have imagined it?

Binding Constants

Calculation and experimental determination of calcium binding by citrate is complex. Partly, all 3 oxygens can accept a proton, so CALCIUM ION VS CITRATE MOLARITYthe acidity of the solution – urine in our case – matters. Partly, binding is complex. As shown in the section below, it involves forming a ring structure and a bi-molecular structure. In general calculations are performed using computer programs.

But simple experiments give a reasonable gauge of the power of citrate to bind calcium. In the figure adapted from Table 2 of the reference at the top of this section, when the molarity of calcium and citrate are equal, at both 2.5 and 5 mmol/l of total calcium (2.5 – grey circles and 5 – black circles in the legend), a common range in urine, only about 1 mmol of calcium is unbound and therefore a free ion that can combine with oxalate or phosphate to make a stone. From the shapes of the graphs, citrate is a powerful binder as the calcium ion falls almost linearly with citrate molarity.

This graph is very approximate. Actual calculations of citrate binding effects have to consider pH, ionic strength, and many varieties of citrate calcium salts. These are part of how supersaturations are calculatedYet for all its simplifications, this graph of ancient data suffices to show what citrate can do as a protection against urine crystallizations of calcium salts like calcium oxalate and calcium phosphate. 

Calcium Citrate Crystal

But this is not a complete story. What if calcium and citrate combine to make a crystal which becomes yet another kind of stone? They can indeed form a crystal, but one which is so soluble it is never a stone risk. Even so, how the crystal forms is a way to show how the molecule binds calcium, which is in itself simply very interesting.

Creation of the Di-Citrate

I have made this structure the featured illustration for the article, but put a copy here for visual convenience. Would you have imagined the two ends of the molecule would bend around to hold the calcium, which makes what was linear into what is, now, a ring?

Just below is another ring, identical in character. Neither is a crystal, merely they are a pair of rings.

But, that odd outcropping of a carbon atom on the original molecule has its charged oxygen, and through another calcium, caught there, the two are linked.

Citrate has two ways to bind calcium. A single molecule can bind one calcium atom. Two citrate molecules together can bind one calcium atom. So the ratio is 1.5 calcium atoms per molecule of citrate (3 atoms/2 citrate molecules).

The Making of a Crystal

How these paired rings make a crystal is not an easy story to tell. Here is a good reference which I will explicate not as a crystallographer, which I am certainly not, but as a narrator telling a good story.

calcium citrate crystal jpeg versioinThe calcium citrate crystal is built up out of repeating units, each of which is a pair of citrate molecules linked by a calcium atom. This ‘di-citrate’ unit has three calcium atoms in it, one in the center, which is unique, and one at each end which mirror each other. These are in the diagram just above.

All three coordinate with 8 oxygen atoms. By this I mean that in addition to the 2 oxygens shown in the simple figure of the di-citrate molecule, oxygens are shared that belong to di-citrate molecules ‘above; and ‘below’  and to the sides so as to make a set of plates like the floors of a parking building.

This complex macrame shows all three calcium atoms. The middle one – calcium 1, at the center of this drawing – relates to 6 oxygens bound to carbon atoms, and to two belonging to water molecules that are pulled into the final structure. The second – at the left lower corner – is coordinated by 8 oxygens bound to carbons, and the third – at the right lower corner, is coordinated with 7 oxygens bound to carbon and one hydroxyl (OH) bound to a carbon (see the simple di-citrate drawing).

This crystal, calcium citrate, is actually a medicinal product (‘Citracal’™) which when swallowed in a pill form dissolves in the gastrointestinal tract to donate calcium and citrate that can be absorbed into the blood. The crystal itself is not found in urine. The medication is of no immediate interest concerning stone disease because one does not use it as a treatment for stones but rather as a supplement for bones. Whether or not it might be helpful in preventing stones would require a trial.

The citrate used for stones is potassium citrate, which is simply the single citrate molecule with its 3 negative charges satisfied by potassium ions or protons.

Why, then, have I troubled you with the elaborate business of citrate calcium binding and crystal formation?

Because it is one way that citrate protects against stones. The molecule binds calcium which is therefore no longer free to combine with oxalate or phosphate to form kidney stones. The crystal calcium and citrate forms does not make stones because it is very soluble. If it were not, citrate would not be a protection against stones but merely the substrate for yet another calcium type stone.

Solubility of Calcium Citrate

What, then, is the evidence for this statement – that the calcium citrate crystal is so soluble that it does not make stones? I have said it several times but have provided you with no proof.

The three oxygens of citrate are partially occupied by protons, and when calcium citrate solubulutythey are they are not available to coordinate with calcium to make the di-citrate and its crystal. Therefore the solubility of citrate will be influenced by the concentration of protons, the acidity of the urine, represented here by pH.

The experiment is done by adding crystals to a simple salt solution, letting them equilibrate with the solution at a constant temperature, and measuring, in this case, the concentration of calcium that is in the solution, having left the crystals as they dissolve.

Two of the three oxygens are ‘weak’ acids which are half saturated with protons at pH values of about 3 and 4, meaning that throughout the range of urine acidity – pH 4.5 to 8 – both are free to bind with calcium. The third is at pH 6.4. One might expect an increase in calcium binding as pH rises above this point, but there is no obvious change in the solubility of the crystal between 5 and above 7.

At pH of 6, the mean for normal urine, the concentration of calcium in solution is about 0.2 mg/ml or 200 mg/liter. Given the atomic weight of calcium – 40- this is 5 mmol/liter. Calcium oxalate crystals dissolved in the same way yield a calcium concentration below 0.005 mg/ml or 5 mg/liter which is about 0.05 mmol/liter. Calcium phosphate crystals give a value of 0.08 mg calcium/ml. 80 mg/liter or 2 mmol/l, less than half of the citrate.

Since calcium and citrate are released from the crystal in proportions of 1.5 calcium per di-citrate, one presumes the equilibrium citrate molarity will be 66% of calcium or 3.3 mmol. Given the molecular weight of citrate is 192 mg/mmol, this amounts to 633 mg/liter of citrate. That is a high concentration of citrate, given that common excretion rates are rarely above 750 mg/day and urine volumes about 1.5 liters a day. Even so, some urine samples almost certainly achieve these concentrations of calcium and citrate on occasion. But equilibrium is not enough to create new crystals; one needs to achieve a higher value so that new crystal nuclei will form. That will be very unlikely for calcium citrate.

So citrate can combine with calcium to remove it from binding with oxalate and phosphate, and form a crystal of considerable solubility. Being very soluble, calcium citrate is rarely if ever found as a kidney stone.

Calcium and Citrate in Urine

calcium - citrate picture

One of two crucial issues about citrate in stone prevention is the relationship between the concentration of calcium and that of citrate. The higher the concentration of citrate compared to calcium, the lower the concentration of unbound calcium, which is free to combine with oxalate or phosphate to make kidney stones.

This graph from our research work shows the difference between urine calcium and urine citrate concentrations for normal people (red), and calcium phosphate (blue) and calcium oxalate (yellow) stone formers over the full day and overnight periods. These two kinds of stones have already been reviewed on this site. 

Normal people have lower urine calcium excretion rates than stone forming patients, but about the same excretion rates for citrate, so the calcium – citrate difference is below 1 mmol/liter. In the graph above which shows free calcium ion at two concentrations of total calcium – 2.5 and 5 mmol/l vs. citrate concentration, when the calcium and citrate concentrations are equal the free calcium is below 2 mmol/liter. When citrate concentration exceeds that of calcium, the free calcium will be lower.

Both of the patient groups have much higher calcium excretions than normal people and because their urine citrate excretions are no higher, and perhaps even lower than among normals, the concentrations of free calcium are much higher, in the range of 2 – 3 mmol/liter.

It is this kind of information which has long made scientists believe that citrate is an important factor in the normal defense against calcium stone formation, and which led to the successful trials which proved that this believe is not unfounded.

What is the Real Science?

The citrate story illustrates all the three forms of scientific research.

Empirical science is what we would call the meticulous measurement of the binding constants between citrate and calcium, and the specific structure of the calcium citrate crystal. It is also what we would call the pretty graph of urine calcium – citrate differences in normal people and stone forming patients.

Applied science is the trials which showed that the intuition of citrate as a treatment was a true intuition. It is indeed a treatment, and that is a fact which time will not alter.

Basic science, however, is not so obvious here. Where in the story do we encounter the passion or curiosity to ask how citrate has come to be in urine.

Certainly citric acid plays a role in biology vastly  – one might say infinitely – greater than that of stone prevention. It is the key molecule in the citric acid cycle which is so well known that I have only to reference it from Wikipedia. Known to schoolboys and schoolgirls everywhere, this cycle is used by all aerobic organisms to generate energy, and is of an extreme ancient origin.

Surely a molecule of such lineage and power is ruled little if at all by the problems of renal crystals. Yet it is handled by the kidneys with considerable finesse as if somehow important to the renal system or – perhaps – as if the renal systems were somehow important in the larger matters of maintaining serum levels of the molecule.

Here is imaginative science. Here is the place where a question of underlying cause comes into focus. Here is where nature presents issues of monumental consequence.






  1. Deirdre Mc Intyre

    You are going to smile doctor because from your articles I have been trying to solve my Shih tzu problem in developing stones! It is a breed prone to them. She was a rescue and has had two surgeries the first had Calicum and struvite stones and the second just Calicum as she is on a strict diet. Her urine is always very concentrated, she does not pee as much as other dogs I know. Her only option seems a third surgery I told my vet about potassium citrate which is available for dogs which he was not aware of and I recently bought it and have been giving it to her but I believe you said existing stones cannot dissolved correct?

    • Fredric Coe, MD

      Hi Deirdre, Dogs get stones and there are scientists who study the matter. The potassium citrate may help but it is hard to know because the urine risk factors are not calibrated for dogs. But if you get even a small sample it can be analysed by commercial vendors for supersaturations which will help. Struvite usually means infection, so that is a separate issue.

  2. terry

    hi. again, thanks for this service.
    does citrate bind to calcium in the gut (as in a calcium citrate supplement) reducing the amount of calcium available to bind with oxalates? how about citric acid (as from lemonade)?
    on a different question, does d3 in calcium supplements influence the binding of calcium and oxaltes?

    • Fredric Coe, MD

      Hi Terry, No, it does not because ingested citrate is absorbed and metabolized to bicarbonate, and that bicarbonate signals the kidneys to release citrate from blood into the urine. Citric acid is useless. Citrate is metabolized as citric acid so it takes up a proton, citric acid already has its protons and its metabolism does not lead to production of bicarbonate. Vitamin D is not known to affect urine oxalate. It may improve calcium absorption but this latter is rarely more than 15% and should be taken with a high calcium diet leaving ample to bind oxalate. Regards, Fred Coe

      • terry

        thanks again. i feel like the jester at the tudor court, trying to dance my way through the complexities of chemistry in your article re: potassium citrate. i am a lacto-ovo vegetarian and eat low oxalates. when i have a meal i suspect is higher that desired in oxalates, i take half a 600 mg. calcium carbonate tablet (without d3). would it be helpful to switch to a calcium citrate supplement, even though all of them seem to have the added d3? also, i enjoy lemon/lime in my water. no harm/no benefit from that? best, terry

        • Fredric Coe, MD

          Hi Terri, It is complex. What I can offer on a site is the general rule but real meal planning and supplements especially need to follow on what was found in your urine and be collaborative with your physicians. Here is a plan for you – if I have not already brought it. Be sure all the steps have been gone over with your physician. They should lead you properly. We have a new article on calcium in the diet, just put up. The invaluable thing your physician brings is an understanding of all this complexity so you can get what you need more easily. Regards, Fred Coe

  3. kim

    Interested in your, Calcium binding by citrate, article, by Fredric Coe, MD. Could you run rainwater through mineralized, chalk like, porous rock, through adsorption, would the molecules now have a net positive charge and leave a negative charge behind in the chalk? Doubly reinforcing the water when it dissolves the chalk. Would the calcium carbonate molecule split, causing a calcium atom with a double positive charge(ion) to be washed away in the water. Would that leave negative ions in the water? Looking for ways to get negative ions for health? Thanks so much…Kim

    • Fredric Coe, MD

      Hi Kim, Things do not quite work that way. If you run pure water – I think that is what you are after in rainwater, through chalk – calcium carbonate, and if the rain is acidic as rain is these days, some of the carbonate will become bicarbonate and release its calcium. The calcium and the bicarbonate will enter the solution. The calcium has two positive charges, the bicarbonate one negative charge, and the water forms a hydronium ion with another negative charge. The charges are all balanced – the sum of the positive and negative charges is always 0. Charge separation is not possible under conditions of ordinary chemistry reactions like this one and only occurs at very high temperatures, or within high voltage electrical fields, neither condition one you might want to be around in. So you can get lots of negative ions anytime you want – dissolve baking soda in water, but you get an equal number of positive ones right in the same place to balance them. Regards, Fred Coe

  4. Chase Naisbitt

    This is a great article. I notice quite a bit of reference to Potassium Citrate which, although is very soluble in water, doesn’t have me convinced as the preferred prescribed form of Citrate. Is it not true that while passing through the digestive tract it will first be blasted with HCl in the stomach then Sodium Bicarbonate in the Duodenum?

    This would convert the very expensive potassium citrate to citric acid then convert it to sodium citrate. This being the case, wouldn’t the popular candies such as warheads (that contain up to 60% citric acid) be just as effective and a fraction of the cost of potassium citrate?

    If you were to go a step further looking at the molar ratios of Potassium Citrate and Citric Acid you would get 1.59 times more citric acid per gram of Potassium Citrate (and enjoy a tasty candy). 🙂

    • Fredric Coe, MD

      Hi Chase, The citrate is metabolized in the Krebs cycle as citric acid, so it takes up a mole of protons per mole of citric acid metabolized. In blood citrate and citric acid are in equilibrium which greatly favors abundance of citrate, but since metabolism is only of citric acid the process consumes protons. These protons come from carbonic acid – the blood buffer is bicarbonate/Carbonic acid – and as they are taken up new bicarbonate is made from CO2 whose partial pressure is regulated by respiration. The GI tract effects are rather neutral as you point out. Citrate is protonated in the stomach to citric acid and regenerated in the duodenum by bicarbonate secretion, but the formulations are usually wax matrix and escape gastric dissolution anyway. If they did or did not the result on acid base balance is about neutral. Once absorbed as citrate, however, the molecule is metabolized as the acid. Giving citric acid itself predictably does nothing to urine citrate because it is simply metabolized as such. Thanks for the outstanding question. Regards, Fred Coe

  5. Hope

    Hi Dr. Coe,
    I have a client with kidney stones and am curious if this tx can be applied for her? She is only on coumadin for meds. She eats low oxalate foods but is frustrated with the list of options. I wondered if is works as a binder in hopes to increase her food choices. What do you think?
    Thanks, Hope Hayes, RD

    • Fredric Coe, MD

      Hi Hope, the trials for stone prevention with potassium citrate emphasized calcium stone formers with reduced urine citrate excretions. They are summarized here. Coumadin would not be an issue. Low oxalate foods are reasonable if her urine oxalate excretion is high, but not otherwise. Regards, Fred Coe, MD

  6. Judi Stratton

    6/21/15 This is strange — For the past two days I’ve noticed that in my poop in the toilet are 2 undissolved potassium citrate pills for each day. They float. To me this does not seem normal. The pills are just going through me whole, so they are not doing any good. Have you ever heard of a situation like this? Please respond. Thank you – Judi Stratton

    • Fredric Coe, MD

      Hi Judi, yes I have heard about this frequently. The 10 mEq (1080 mg) large pills are wax matrix slow release, and the shell remains intact despite the contents leaving the pill and entering the bloodstream. I have noticed the 5 mEq pills – smaller and shiny surface – seem to be coated and may not release their contents. But follow up 24 hour testing, which is always appropriate when a medication has been prescribed, can tell what has happened. Compared to your initial evaluation, the 24 hour urine should show changes from the pills: increased urine potassium, increased urine pH, and a fall in urine ammonium ion as compared to the urine sulfate ion. Your physician knows to look for these changes as evidence of absorption of the active medication. The urine citrate itself is a less exacting sign because it may not increase even when the drug is fully absorbed. I am sure your physician has already made these observations and I would simply call and be sure the pills are working. Incidentally, you posted two nearly identical comments within several minutes, and I took the liberty of leaving only one on the site. Regards, Fred Coe


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