Binding site pocket

Almaula, N., Ebersole, B.J., Zhang, D., Weinstein, H., Sealfon, S.G. Mapping the binding site pocket of the serotonin 5-hydroxytryptamine2A receptor. Ser3.36(159) provides a second interaction site for the protonated amine of serotonin but not of lysergic acid diethylamide or bufotenin, J. Biol. Chem. 1996,271(25), 14672-5. 

Almaula et al. [72] investigated the binding site pocket of the cloned human 5-HT2A receptor expressed in COS-1 cells using mutation studies and computational dynamic simulations. It was shown that the full agonist 5-HT binds with its cationic primary amine group to Asp-155 (helix 3) and by a hydrogen-bond type interaction with Ser-159 (helix 3) whereby serine acts as a H-acceptor. 

The following abbreviations were used S3, S2, SI, ST, and S2 are the conventional labels for the HlV l protease binding site pocket (Ref. 11) for example, SI and ST are located at the catalytic site (binding the proximal and distal side chains from the scissile bond). Amino acid residues in the vicinity of the CoMFA region are numbered as in HlV-1 protease. Detrimental contributions indicated by beneficial contributions by +. Double minus or double plus mean very detrimental or beneficial, respectively. Up, down, front, and back refer qualitatively to the binding site as conveniently viewed see Ref. 122. One-letter notation for amino acids ... 

Figure 4.8 The active site in all a/p barrels is in a pocket formed by the loop regions that connect the carboxy ends of the p strands with the adjacent a helices, as shown schematically in (a), where only two such loops are shown, (b) A view from the top of the barrel of the active site of the enzyme RuBisCo (ribulose bisphosphate carboxylase), which is involved in CO2 fixation in plants. A substrate analog (red) binds across the barrel with the two phosphate groups, PI and P2, on opposite sides of the pocket. A number of charged side chains (blue) from different loops as welt as a Mg ion (yellow) form the substrate-binding site and provide catalytic groups. The structure of this 500 kD enzyme was determined to 2.4 A resolution in the laboratory of Carl Branden, in Uppsala, Sweden. (Adapted from an original drawing provided by Bo Furugren.)...

The binding site is located at the tip of the subunit within the jelly roll structure (Figure 5.23). The sialic acid moiety of the hemagglutinin inhibitors binds in the center of a broad pocket on the surface of the barrel (Figure 5.24). In addition to this groove there is a hydrophobic channel that can accomodate large hydrophobic substituents at the C2 position of sialic acid (Figures 5.22 and 5.24). 

Serine proteinases such as chymotrypsin and subtilisin catalyze the cleavage of peptide bonds. Four features essential for catalysis are present in the three-dimensional structures of all serine proteinases a catalytic triad, an oxyanion binding site, a substrate specificity pocket, and a nonspecific binding site for polypeptide substrates. These four features, in a very similar arrangement, are present in both chymotrypsin and subtilisin even though they are achieved in the two enzymes in completely different ways by quite different three-dimensional structures. Chymotrypsin is built up from two p-barrel domains, whereas the subtilisin structure is of the a/p type. These two enzymes provide an example of convergent evolution where completely different loop regions, attached to different framework structures, form similar active sites. 

Active site of an enzyme is the binding site where catalysis occurs. The structure and chemical properties of the active site allow the recognition and binding of the substrate. The active site is usually a small pocket at the surface of the enzyme that contains residues responsible... 

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