Geometry of the binding site

However, as said before, even the most elegant description of steric bulk of a substituent cannot cope with the problem of the unknown geometry of the binding site and its steric constraints. The quantitative description of steric effects is a puzzling problem even in the case of known 3D structures of the protein, due to... 

Figure 6 exemplifies the information content provided by each method. Thus, while the MCD spectra of Cd-MTs afford the information about the geometry of the binding sites (A-terms if tetrahedral CdS4 units are present), the conformational changes accompanying the cluster formation and the presence of a cluster (exciton splitting) is provided by the CD studies. Combination of CD and MCD techniques has been used in a number of structural studies of Zn,Cd or Cd-MTs from different species [65-73]. 

The crystal structure of poplar apoplastocyanin has been reported at 1.8 A resolution [42]. The structure closely resembles that of the holoprotein, and positions of the Cu-binding residues are different by only 0.1-0.3 A. Tetrahedral coordination, with proportionately larger metal-ligand bond distances, is also observed on replacing the Cu by Hg(II) [43]. This suggests that the irregular geometry of the active site is imposed on the metal atom by the polypeptide... 

For +2 cations such as zinc(ll) and cadmiunXIl) each metallothionem molecule contains up to seven metal atoms. X-ray studies indicate that the metal atoms are in approximately tetrahedral sites bound to the cysteine sulfur atoms. The soft mer-cury(JI) ion has a higher affinity for sulfur and will displace cadmium from mefallothio-nein. At first the mercury ions occupy tetrahedral sites but as the number increases, the geometries of the metal sites and protein change until about nine Hg(II) atoms are bound in a linear (S—Hg—S) fashion.92 Up to twelve + I cations such as copper(l) find silverfUcan bind per molecule, indicating fi coordination number lower than four, probably three (see Problem 12.34). 

A variation is observed for E. coli thioredoxin reductase. The reducible disulfide and the NADPH binding site are both on the same side of the flavin rather than on opposite sides as in Fig. 15-12.190/259 Mercuric reductase also uses NADPH as the reductant transferring the 4S hydrogen. The Hg2+ presumably binds to a sulfur atom of the reduced disulfide loop and there undergoes reduction. The observed geometry of the active site is correct for this mechanism. 

The calcium sites in troponin C have been studied by X-ray absorption near edge structure (XANES).244 In all four cases, Ca2+ appears to be coordinated to carboxylate and carbonyl groups, and no structural differences could be found between the two classes of sites. Binding of Mg2+ causes a distortion of the geometry of the calcium site. Thus, the reduced affinity for Ca2+ of the Ca2+-Mg2+ sites in the presence of Mg2+ may not simply be due to competition with Mg2+, but due to some conformational change induced at these sites by Mg2+. The similarity of all four Ca2+ sites means that local bonding effects do not explain the inability of Mg2+ to bind to the calcium-specific sites I and II. The XANES of parvalbumin differs from that of troponin C. 

Distinguish between the primary, secondary and tertiary structure of proteins. Which is usually responsible for the geometry and properties of the substrate binding site How are the properties of the binding site reflected by the induced fit model ... 

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