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Monday, January 23, 2012

Monday's Molecule #156

This is one of the most important molecules on Earth. Without it we wouldn't be around and neither would most species. The revised structure is shown here. The one shown in the textbooks is wrong and this includes my own recently published edition of Principles of Biochemistry. Oops!

You need to identify the molecule, including the part with the white carbon atoms. You also need to specify how this molecule differs from the one shown in most textbooks.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is the iron-sulfur-molydenum cluster with bound homocitrate. The central atom was thought to be nitrogen but recent work has shown that it is most likely carbon. The cluster is in the active site of bacterial nitrogenase, an enzyme responsible for fixing atmospheric nitrogen and converting it to ammonia. This is a key part of the nitrogen cycle. The winner is David J. Schuller. I don't know if he will come for lunch.

Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin


  1. Iron-Molybdenum-Sulfur-Homocitrate cluster from some nitrogenease, obviously. I am guessing the error has something to do with citrate stereochemistry but I don't have time today for googling and figuring it out.

  2. That is the FeMo cofactor of nitrogenase.

    "the FeMo cofactor, is a [Mo:7Fe:9S:X]:homocitrate cluster, the largest and most complex biological metal center known to date." (from reference 1 cited below)

    The white carbons belong to 3-HYDROXY-3-CARBOXY-ADIPIC ACID (homocitrate); except for those in a ring with the two nitrogens, which belong to a histidine residue of the protein.

    The atom liganding Fe2-7 is a carbon, not a nitrogen as previously thought.

    T. Spatzal, et al, "Evidence for Interstitial Carbon in Nitrogenase FeMo Cofactor"
    Science 18 November 2011:
    Vol. 334 no. 6058 p. 940
    DOI: 10.1126/science.1214025

    Abstract: "The identity of the interstitial light atom in the center of the FeMo cofactor of nitrogenase has been enigmatic since its discovery. Atomic-resolution x-ray diffraction data and an electron spin echo envelope modulation (ESEEM) analysis now provide direct evidence that the ligand is a carbon species."

    K.M. Lancaster, et al. "X-ray Emission Spectroscopy Evidences a Central Carbon in the Nitrogenase Iron-Molybdenum Cofactor"
    Science 18 November 2011:
    Vol. 334 no. 6058 pp. 974-977
    DOI: 10.1126/science.1206445

  3. The iron-molybdenum cofactor of the nitrogenase complex - required for the entry of molecular nitrogen into the biosphere

    The part with the white atoms is homocitrate (according to Lehninger 5th ed).

    Difference? Compared to the structure given in Lehninger 5th edition, this molecule has an SH-group attached to the left hand side in the diagram (a total of 10 rather than 9 S).

  4. Molecule # 156 is the molybdenum nitrogenase cofactor, on which all the ecosphere relies for the bulk of its nitrogen fixation. The new discovery is the fact that it contains a central "interstitial" carbon atom. As for the white carbon atoms, from this perspective, all we can say is that it contains an imidazole ring. Although histidine (which contains an imidazole ring) is cited as a ligand for the molybdenum atom in this molecule (along with homocitrate), one can not be sure, from the structure shown, about how they are bound to the other atoms. Besides, if it were histidine, it should contain one more carbon and one more nitrogen atom.

  5. Looks like the FeMoco cofactor from the nitrogenase enzyme, but the ligands are all truncated (HS instead of Cys, glycolic acid instead of homocitric, and imidazole in place of His) as though someone isolated it for Xray crystallography. The difference would be the carbon atom as the central ligand in the middle of the iron atoms, instead of nitrogen as previously reported?

  6. Being sadly ignorant of biochemisty (indeed, of chemistry as it's been a long long time since first year), I've no hope of determining the actual molecule. But I remember comment that in the early earth Molybdenum might have been a limiting factor in the growth of eukaryotic life, as it is needed for fixing nitrogen. After a little google-cheating I conclude that the above is a nitrogenase.

    William Hyde

  7. It is the Iron Molybdenum cofactor (FeMo-cofactor) of the MoFe-protein, part of the active site of nitrogenase. The organic part is homocitrate. It was thought that the small central atom was nitrogen (before that, a paper from 1992 referred to it as a "bridging ligand"), but is now known to be carbon.

  8. OK, no one is stepping up, so I'll take a try: it is the iron-molybdenum cofactor (FeMoco) of the nitrogenase enyme that Azotobacter vinelandii uses to fixes atmospheric nitrogen gas into ammonia, thus making nitrogen biologically available for most other species. The carbon-containing structures off the molybdenum are homocitrate and histidine ligands. The atom surrounded by irons was recently unambiguously identified as carbon; previously, it was thought that it could have been nitrogen or oxygen.

  9. Look carefully guys, the textbook ligand is homocitrate, but theres no homocitrate in the structure above. Count the atoms on the right hand side, its C2H2O3 (glycolic acid doubly deprotonated) and C3H4N2 (imidazole) as I stated above.

    (btw I cant make the lunch date, but Ill happily accept any "Pedantic Chemist is Boring yet Technically Correct" awards you happen to have lying around)

    1. You are correct. The His and homocitrate structures are not correct.

      You could share the prize except that you used a pseudonym. You get the "pedantic anonymous chemist" award as a consolation prize. :-)

  10. The atom liganding Fe2-7 is a carbon, not a nitrogen as previously thought.

    That's really cool! Discrimination between N and C at 1.0A resolution is very nice. I didn't think it's going to be convincing but it is, in fact, almost rock solid.