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My understanding: Transition (d-block) metals, as found in intracellular proteins, are limited to about 10 elements including amongst others Fe, Ni, and Cu. Due to the reductive environments inside cells, they are usually/expected to be found with an oxidation state of +2 (?). However, the number of bonds that coordinate the metal, assuming that you know that the oxidation state is +2, is not completely certain (?).

Confusion about bond and coordination: As the d-orbital of e.g. Fe(II) is not completely filled it can be considered somewhat reactive/unpredictable, and we cannot for sure say what coordination it will have in an enzyme (?). Or, is there some sort of general assumption we can make about its coordination based on its oxidation number (i.e. +2)? As I was looking for literature on the matter I stumbled on the chemistry stack exchange answers regarding ‘bonds in coordination complexes’ which used Fe(II) as an example of how Pauling’s Principle could be applied to simplify how metals are coordinated.

A brief summary of this answers would include that coordinating residues can be thought to contribute ½ electron to the coordination of Fe(II); and thus, Fe(II) would typically have four coordinating interactions while Fe(III) would have six coordinating interactions, in order to cancel the charge.

Summary of question(s): If my statements above are correct, then it could be generally assumed that all +2 metals in enzymes, such as Fe(II) , are coordinated by four groups? Furthermore, the coordinating bonds are considered dative (i.e. not entirely ionic)? Very speculatively, could it also be assumed that Fe(II) would typically be in a tetrahedral complex (why/why not)?

*update based on comments: Octahedral coordination of Fe(II) was mentioned as classical example in heme enzymes, while it is also known that non-heme enzymes can e.g. coordinate Fe(II) with three residues and a water molecules in a tetrahedral conformation. It could therefore be reasoned that coordination of the metal (e.g. tetrahedra vs octahedral) is related to enzyme function and evolution over time, and not so much the oxidation state of the metal?

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    $\begingroup$ Pauling's electroneutrality thingy is not really widely used anymore; it's a very rough rule of thumb and one should not draw generalisations from it. Fe(II) is very commonly octahedral and the factors that determine tetrahedral vs octahedral (& other shapes) coordination can be quite complicated. Hemoglobin is the most common example of a Fe(II) metalloprotein and the coordination geometry is octahedral (although strictly speaking, only one of the bonds is to an amino acid residue – the 'proximal histidine'). $\endgroup$
    – orthocresol
    Aug 28 '20 at 9:23
  • $\begingroup$ Thanks, so this add to the fact that transition-state metals cannot be so early understood, and that one should not assume simple 'rules of thumb' for e.g. Fe(II). Im still a bit confused about coordinatin: I know (non-heme) enzymes with Fe(II) that have three amino acids and a water molecule coordinating it (tetrahedral), while heme-enzymes with Fe(II), like you mention, are octahedral. There seems to be no real pattern – it is more a case-by-case scenario that has to be experimentally validated? $\endgroup$ Aug 28 '20 at 9:35
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    $\begingroup$ I think sometimes it is more unambiguous. For example, Zn(II) is pretty much always tetrahedral, as far as I know. But Fe(II) can be a bit of a chameleon, even outside of proteins. I'm rusty on the (very fascinating) bioinorganic chemistry details, but I do suspect the function of the protein can sometimes lend a clue as to why certain geometries, etc. are adopted. After all, the metal environment (and indeed the choice of metal) have been "selected" through many years of evolution. $\endgroup$
    – orthocresol
    Aug 28 '20 at 9:41
  • $\begingroup$ Functional evolution in terms of metal coordination in enzymes is a good point, I will update the question a bit with this reflection. Thanks! $\endgroup$ Aug 28 '20 at 9:47
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    $\begingroup$ It's further complicated by the fact that many metalloproteins are redox active, so the oxidation state of the metal changes between two states while still coordinated to the protein $\endgroup$
    – Andrew
    Aug 28 '20 at 12:17

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