Is the Fe in the reaction center of bacteria light-harvesting system bounded or free atom?


After reading the comments in the first answer, I believe OP's question is this:

What kind of bond occurs in the Fe of the reaction center of bacteria light-harvesting system?

Before continuing, it's worth mentioning that an ionic bond is a kind of bond, and that atom would not be considered free (whatever that means) even if its bonds were only ionic ones.

However, to make things here even more unequivocal, the bonds of that Fe are covalent bonds (thus, that atom is not free under any definition...).

According to the Protein Data Bank in Europe, this is the x-ray high resolution structure of the photosynthetic reaction center from Rhodobacter sphaeroides at pH 10, zoomed at the portion that contains the Fe (link here):

enter image description here

You can see that the Fe has 5 bonds, thus summarised:

[SQUARE_PYRAMIDAL] - HIS 190L - HIS 219M - HIS 230L - GLU 234M - HIS 266M

And what kind of bond are those?

According to the same PDBE entry, they are covalent. Have a look at the color code in this page: http://www.ebi.ac.uk/pdbe-site/pdbemotif/?tab=boundmolecule&pdb=2uxj&ligandCode3letter=FE

Here is a screenshot, in case the link above doesn't work. Have a look at the 5 red bonds (red represents covalent... not very legible, I know):

enter image description here

Source: Protein Data Bank in Europe

  • $\begingroup$ I would argue that the Fe is bound as a (coordination) complex, as is the case with most metal ions in porteins. This bond is not strictly a covalent bond (the actual physics are actually quite complicated) as none of the electrons forming the bond come from the metal/iron atom itself. $\endgroup$ – Nicolai May 29 '17 at 7:27
  • $\begingroup$ I know what is a coordinate bond, I used to teach that. However, a coordinate bond is a kind of covalent bond (I would like a reference to "this bond is not strictly a covalent bond"). Thus, it seems to me that the answer remains the same. $\endgroup$ – user24284 May 29 '17 at 8:14
  • $\begingroup$ On top of that, PDBE explicitly says covalent bond. $\endgroup$ – user24284 May 29 '17 at 8:43
  • 1
    $\begingroup$ I guess it's mostly a matter of definition, if you classify a coordination bond as a subtype of covalent bond or as it's own type. My chemistry professor from university was arguing for latter version, so that's how I see it. Also wikipedia does not list a coordination bond as a type of covalent bond. $\endgroup$ – Nicolai May 29 '17 at 8:44
  • $\begingroup$ I see. Indeed, it depends on the definition. However, the same wikipedia lists the coordinate as coordinate covalent bond $\endgroup$ – user24284 May 29 '17 at 8:49

I know no examples of free iron atoms serving active physiological functions within living organisms. Iron, as with other metals, are generally in their ionic state. As such, they are attracted and held in position by negative, or partial negative, charges on nearby atoms. Sometimes these are from the sidegroups of proteins but often the negative charges bonding the metals are on specialized molecules such as the poryphrin ring in hemoglobin whic contains an iron ion in the center, held in place by four nitrogen atoms like a gem in a ring.

The principal metal ion in photosynthesis is magnesium. Just as with the iron in hemoglobin, it is centered in a poryphrin ring. This is also true of the chlorophyl in bacteria. But there is also an iron ion associated with the reaction center. Apparently this is "connected" to the P870 bacteriochlorophyl molecule. Here is the article: http://photobiology.info/Jones.html

You can view this for yourself. Here's a link to the molecule in question at the Protein Data Bank (instructions follow): http://www.rcsb.org/pdb/explore.do?structureId=2BOZ

On the left side is a viewing window where you can see various representations of the protein and any associated molecules (ligands). This won't help because the Fe will be hard to pick out. Scroll near the bottom of the page and you will see iron (FE) listed as one of the ligands. In that row, in the far right column, click on "NGL". In case you got lost, here's the direct link: http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=2BOZ&preset=ligandInteraction&sele=[FE]

That's the Fe with the big orange glow. Notice how it's held in place by 4 nitrogens plus a carboxyl group. Click on any "stick" making up one of those nitrogen containing structures. Notice, in the window's upper left, the label for this begins with "HIS". This stands for histidine, an amino acid. Indeed, every one of these goups surrounding the Fe is an amino acid belonging to the chlorophyll protein.

So, unlike the Fe in hemoglobin, this Fe is attached to the protein directly.

  • $\begingroup$ Thank you for the reply. But a few days ago a professor in Germany told me it is not bounded? What follows is her reply, did I miss interpreted her words? =================The non-heme iron can be exchanged, eg. against zinc. It is like a pearl in a shell. In contrast to this, the iron in the cytb556 protein subunit is bound by two subunits (alpha and beta) and coordinated by two histidines. $\endgroup$ – latra Jan 29 '17 at 2:52
  • $\begingroup$ You said "The principal metal ion in photosynthesis is magnesium"? Is it so? Ion is not the principal metal? Then, what is its function? $\endgroup$ – latra Jan 29 '17 at 2:53
  • $\begingroup$ So, the Fe is bounded? Has it a fixed orientation with the RC and the LH1? I think the answer is yes? My question is, what is its orientation? $\endgroup$ – latra Jan 29 '17 at 2:56
  • $\begingroup$ I checked the NGL link you provided. I agree the Fe is "held in place by 4 nitrogens plus a carboxyl group" (quoted as you said) But it does not seems to belong to other structure? But you said it is BOUNDED? Sorry if my question is naive. I do not understand chemistry. I did not studied chemistry after university. I understand only high-school chemistry. $\endgroup$ – latra Jan 29 '17 at 3:04
  • $\begingroup$ So, is the magnesium in chlorophyll bounded or not? $\endgroup$ – latra Jan 29 '17 at 3:06

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