Iron atomic coordinates

A brief historical note on the structure of the iron-sulfur clusters in ferredoxins is relevant. After the first analytical results revealed the presence of (nearly) equimolar iron and acid-labile sulfur, it was clear that the metal center in ferredoxins did not resemble any previously characterized cofactor type. The early proposals for the Fe S center structure were based on a linear chain of iron atoms coordinated by bridging cysteines and inorganic sulfur (Blomstrom et al., 1964 Rabino-witz, 1971). While the later crystallographic analyses of HiPIP, PaFd, and model compounds (Herskovitz et al., 1972) demonstrated the cubane-type structure of the 4Fe 4S cluster, the original proposals have turned out to be somewhat prophetic. Linear chains of sulfide-linked irons are observed in 2Fe 2S ferredoxins and in the high-pH form of aconitase. Cysteines linked to several metal atoms are present in metallothionein. The chemistry of iron-sulfur clusters is rich and varied, and undoubtedly many other surprises await in the future. 

The main metalloporphyrin in the body is heme, which has a ferrous Fe iron atom coordinated by protoporphyrin DC... 

The tetranuclear iron alkoxide halides (see Table 12.23) were supposed to possess the cubane-like or Ti4(OMe)i4 type structures. The Mossbauer spectroscopy indicated the presence of 2 types of iron atom coordination in Fe4Hal6(OMe)6 4MeOH and only one kind of octahedral arrangement in FeCl(OR)2 and Fe4Hal3(OMe)9. For the 2 latter products the layered structures of the Al(OH)3 type were also proposed [867, 1065]. 

It should also be noted that any metal ions coordinated to a protein may contribute to the maximum charge. A ferric iron atom coordinated to a heme protein, for example, normally bears a charge of -M at low pH. Phosphate groups, as previously mentioned, would have a charge of —1 at the acid end point. These charges, where present, will all make a contribution to SA+. 

Heme An essential metaUoorganic cofactor, consisting of one ferrous iron atom coordinated within a tetrapyrrole ring, protoporphyrin IX. 

Rubredoxin constitutes the simplest class of iron-sulfur proteins with one iron atom coordinated by four cysteinyl residues and containing no labile sulfur. They are present in aerobes as well as in anaerobic organisms but despite their widespread occurence their general function has not yet been determined, although the rubredoxin isolated from Pseudomonas oleovorans has been shown to be active in the co-hydroxy-lation reaction41 and a highly specific NADH—H+ rubredoxin-oxido-reductase is present in Desulfovibrio gigas39 ... 

Several complexes have been prepared containing tetrahedral iron atoms coordinated to two molybdenums through two pairs of 22-sulfido ligands. [NH4]2[MoS4] reacts... 

In order to clarify the complete procedure, it will be exemplified step by step, using the case of the Desulforedoxin homo-dimer (case 12). Finally the results of all other test cases will be summarized in Table 2. Desulforedoxin, isolated from the sulfate reducing bacteria Desulfovibrio gigas, is a small dimeric protein formed by two identical subimits of 4 kDa each, containing an iron atom coordinated by four cysteinyl residues, which is responsible for the oxido-reduction properties of the protein. 

Ferrocene Figure 2-47) provides a prime ex.ample of multi-haptic bonds, i.e, a situation where the electrons that coordinate the cyclopentadienyl rings with the iron atom arc contained in molecular orbitals delocalised over the iron atom and the 10 carbon atoms of the cyclopentadienyl rings [82. ... 

Ferrocene (Figure 2-61a) has already been mentioned as a prime example of multi-haptic bonds, i.c, the electrons tlrat coordinate tire cyclopcntadicnyl rings with the iron atom are contained in a molecular orbital delocalized over all 11 atom centers [811, for w hich representation by a connection table having bonds between the iron atom and the five carbon atoms of cither cyclopcntadicnyl ring is totally inadequate. 

Figure 1.9 Examples of functionally important intrinsic metal atoms in proteins, (a) The di-iron center of the enzyme ribonucleotide reductase. Two iron atoms form a redox center that produces a free radical in a nearby tyrosine side chain. The iron atoms are bridged by a glutamic acid residue and a negatively charged oxygen atom called a p-oxo bridge. The coordination of the iron atoms is completed by histidine, aspartic acid, and glutamic acid side chains as well as water molecules, (b) The catalytically active zinc atom in the enzyme alcohol dehydrogenase. The zinc atom is coordinated to the protein by one histidine and two cysteine side chains. During catalysis zinc binds an alcohol molecule in a suitable position for hydride transfer to the coenzyme moiety, a nicotinamide, [(a) Adapted from P. Nordlund et al., Nature 345 593-598, 1990.)...

Inspection of the citrate structure shows a total of four chemically equivalent hydrogens, but only one of these—the pro-/J H atom of the pro-i arm of citrate—is abstracted by aeonitase, which is quite stereospecific. Formation of the double bond of aconitate following proton abstraction requires departure of hydroxide ion from the C-3 position. Hydroxide is a relatively poor leaving group, and its departure is facilitated in the aeonitase reaction by coordination with an iron atom in an iron-sulfur cluster. 

FIGURE 21.18 (a) The Cn site of cytochrome oxidase. Copper ligands inclnde two histidine imidazole groups and two cysteine side chains from the protein, (b) The coordination of histidine imidazole ligands to the iron atom in the heme a center of cytochrome oxidase. 

The simplest NHIP is rubredoxin, in which the single iron atom is coordinated (Fig. 25.9a) to 4 S atoms belonging to cysteine residues in the protein chain. It differs from the other Fe-S proteins in having no labile sulfur (i.e. inorganic sulfur which can be liberated as H2S by treatment with mineral acid sulfur atoms of this type are not part of the protein, but form bridges between Fe atoms.)... 

Cp(CO)2Re(THF) forms the complex 105 upon reaction with thiophene (89JA8753, 910M2436). Similar species are known for 2- and 3-methyl-, 2,5-dimethyl, and tetramethylthiophene (91IC1417). Thiophene in 105 is S-coordi-nated, and the sulfur atom is pyramidal. Treatment of 105 with Fc2(CO)9 produces 106, where the thiophene ligand is bridge-coordinated via the sulfur atom to rhenium and four carbon atoms of the dienic system with iron (the coordination mode). The pyramidal nature of the sulfur atom is preserved. The -coordination of thiophene separates the dienic and sulfur counterparts of the ligand and decreases the TT-electron delocalization, which leads to the enhanced basicity of the sulfur atom. 

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