Zinc atom

Figure Bl.8.4. Two of the crystal structures first solved by W L Bragg. On the left is the stnicture of zincblende, ZnS. Each sulphur atom (large grey spheres) is surrounded by four zinc atoms (small black spheres) at the vertices of a regular tetrahedron, and each zinc atom is surrounded by four sulphur atoms. On the right is tire stnicture of sodium chloride. Each chlorine atom (grey spheres) is sunounded by six sodium atoms (black spheres) at the vertices of a regular octahedron, and each sodium atom is sunounded by six chlorine atoms.

Potassium chloride actually has the same stnicture as sodium chloride, but, because the atomic scattering factors of potassium and chlorine are almost equal, the reflections with the indices all odd are extremely weak, and could easily have been missed in the early experiments. The zincblende fonn of zinc sulphide, by contrast, has the same pattern of all odd and all even indices, but the pattern of intensities is different. This pattern is consistent with a model that again has zinc atoms at the comers and tlie face centres, but the sulphur positions are displaced by a quarter of tlie body diagonal from the zinc positions. 

Unlike cadmium and mercury and, in fact, all metals of Group II, zinc dissolves readily in alkalis forming zincates. in which the zinc atom is contained in a complex hydroxo-anion, for example ... 

Another source of departure from stoichiometry occurs when cations are reduced, as for example in tire reduction of zinc oxide to yield an oxygen-defective oxide. The zinc atoms which are formed in tlris process dissolve in the lattice, Zn+ ions entering interstitial sites and the coiTesponding number of electrons being released from these dissolved atoms in much the same manner as was found when phosphorus was dissolved in the Group IV semiconductors. The Kroger-Viirk representation of dris reduction is... 

Why is this relevant to the diffusion of zinc in copper Imagine two adjacent lattice planes in the brass with two slightly different zinc concentrations, as shown in exaggerated form in Fig. 18.5. Let us denote these two planes as A and B. Now for a zinc atom to diffuse from A to B, down the concentration gradient, it has to squeeze between the copper atoms (a simplified statement - but we shall elaborate on it in a moment). This is another way of saying the zinc atom has to overcome an energy barrier... 

In order for these atoms to actually climb over the barrier from A to 6, they must of course be moving in the right direction. The number of times each zinc atom oscillates towards B is v/6 per second (there are six possible directions in which the zinc atoms can move in three dimensions, only one of which is from A to B). Thus the number of atoms that actually jump from A to B per second is... 

But, meanwhile, some zinc atoms jump back. If the number of zinc atoms in layer B is Ug, the number of zinc atoms that can climb over the barrier from B to A per second is... 

Thus the net number of zinc atoms climbing over the barrier per second is... 

The second mechanism is that of vacancy diffusion. When zinc diffuses in brass, for example, the zinc atom (comparable in size to the copper atom) cannot fit into the interstices - the zinc atom has to wait until a vacancy, or missing atom, appears next to it before it can move. This is the mechanism by which most diffusion in crystals takes place (Figs. 18.7 and 10.4). 

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.)...

Carboxypeptidases are zinc-containing enzymes that catalyze the hydrolysis of polypeptides at the C-terminal peptide bond. The bovine enzyme form A is a monomeric protein comprising 307 amino acid residues. The structure was determined in the laboratory of William Lipscomb, Harvard University, in 1970 and later refined to 1.5 A resolution. Biochemical and x-ray studies have shown that the zinc atom is essential for catalysis by binding to the carbonyl oxygen of the substrate. This binding weakens the C =0 bond by... 

Figure 4.19 Schematic and topological diagrams for the structure of the enzyme carboxypeptidase. The central region of the mixed p sheet contains four adjacent parallel p strands (numbers 8, 5, 3, and 4), where the strand order is reversed between strands 5 and 3. The active-site zinc atom (yellow circle) is bound to side chains in the loop regions outside the carboxy ends of these two p strands. The first part of the polypeptide chain is red, followed by green, blue, and brown. (Adapted from J. Richardson.)...

Figure 4.20 Detailed view of the zinc environment in carboxy-peptidase. The active-site zinc atom is bound to His 69 and Glu 72, which are part of the loop region outside P strand 2. In addition, His 196, which is the last residue of P strand 5, also binds the zinc.

This is precisely where the catalytically essential zinc atom is found. This zinc atom is located precisely at this switch point, where it is firmly anchored to the protein by three side-chain ligands, His 69, Glu 72, and His 196 (Figure 4.20). The last residue of p strand 3 is residue 66, so the two zinc ligands His 69 and Glu 72 are at the beginning of the loop region that connects this p strand with its corresponding a helix. The last residue of p strand 5 is the third zinc ligand. His 196. 

In this structure the loop regions adjacent to the switch point do not provide a binding crevice for the substrate but instead accommodate the active-site zinc atom. The essential point here is that this zinc atom and the active site are in the predicted position outside the switch point for the four central parallel p strands, even though these p strands are only a small part of the total structure. This sort of arrangement, in which an active site formed from parallel p strands is flanked by antiparallel p strands, has been found in a number of other a/p proteins with mixed p sheets. 

In contrast to the zinc-containing DNA-binding domains described so far, the GAL4 family contains a cluster of two zinc atoms liganded to six cysteine residues, and two of these cysteines (residues 11 and 28) are bound to... 

A unique feature of the interaction of the hormone and PLR is at the beginning of the F-G loop in the C-terminal domain. In HGR the sequence is Arg-Asn-Ser whereas in PLR it is Asp-His-deletion. This loop interacts with His 18 and Glu 174 of the hormone. In PLR the orientation of this loop is such that the Asp and His residues, in combination with His and Glu from the hormone, form a strong binding site for a zinc atom that links the hormone and the receptor (Figure 13.23b). The presence of zinc increases the affinity of the hormone for the receptor in vitro by a factor of 10,000. As shown by mutagenesis studies His 18 and Glu 174 of the hormone are important for the tight binding to PRL but not to GHR. 

The classic zinc fingers, the DNA-binding properties of which are discussed in Chapter 10, are small compact domains of about 30 residues that fold into an antiparallel p hairpin followed by an a helix. All known classic zinc fingers have a zinc atom bound to two cysteines in the hairpin and two histidines in the helix, creating a sequence motif common to all zinc finger genes. In the absence of zinc the structure is unfolded. 

Figure 17.15 Schematic diagrams of the main-chain conformations of the second zinc finger domain of Zif 268 (red) and the designed peptide FSD-1 (blue). The zinc finger domain is stabilized by a zinc atom whereas FSD-1 is stabilized by hydrophobic interactions between the p strands and the a helix. (Adapted from B.I. Dahiyat and S.L. Mayo, Science 278 82-87, 1997.)...

The situation is different for other examples—for example, the peptide hormone glucagon and a small peptide, metallothionein, which binds seven cadmium or zinc atoms. Here large discrepancies were found between the structures determined by x-ray diffraction and NMR methods. The differences in the case of glucagon can be attributed to genuine conformational variability under different experimental conditions, whereas the disagreement in the metallothionein case was later shown to be due to an incorrectly determined x-ray structure. A re-examination of the x-ray data of metallothionein gave a structure very similar to that determined by NMR. 

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