Binding, geometry

Barna TM, H Khan, NC Bruce, I Barsukov, NS Scrutton, PCE Moody (2001) Crystal structure of pentaeryth-ritol tetranitrate reductase flipped binding geometries for steroid substrates in different redox states of the enzyme. J Mol Biol 310 433-447. 

Figure 2. Stereoview of the allosteric binding site of fructose 1,6-bisphosphatase and the binding geometry of AMP (yellow).

Returning to Fig. 10, because the majority of the alkyl groups are flexible and because the interfacial electrostatic binding geometries are unknown, the rate of falloff of kbET or Hab with semiconductor/molecule separation distance cannot be evaluated quantitatively. A curious finding that remains unexplained is that the falloff with osmium complexes is considerably weaker than with ruthenium species. Finally, although the injection reaction was not the focus of the study, spacers clearly do decrease its rate, as shown, for example, by an increase in emission quantum yield (decrease in injection efficiency) with the largest spacers. 

Figure 1. Binding geometry of CHC1, adsorbed Figure 2. Observed and simulated heats of...

The conclusion that can be drawn from each of these correlations is that the P2 residues of the inhibitors, and only those, interact with the protein active site in the same manner as in the transition state. The tightness of the correlation may indicate the degree to which the binding geometries remain constant... 

Even simple protonated tripodal amines such as tren (2,2, 2,-tr/s(aminoethyl)amine, 4.6) itself exhibit interesting anion-binding geometries. The X-ray crystal structure of tren-HBr (Figure 4.11a) shows the bromide anion interacting with all three terminal amine groups, one of which is protonated.16... 

A comparison of the binding geometries of the three halide complexes with 6 is shown in Figure 13. Here the two most common geometries that are repeated in other cryptand complexes are observed, tetrahedral (Figure 13A - C) and octahedral (Figure 13D). 

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