Our results revealed that the characteristic substrate-binding pocket composed of hydrophobic amino acid residues ensures substrate docking for the stereospecific reaction of RrQR in spite of its loose interaction with the substrate.
SMU.440 also shares a similar binding pocket composed primarily of residues with aromatic and acidic side-chains, which points to a potential binding of a polyketide-like molecule.
The immediate effect of the cyclopentyl group within the binding site is measured by the time series of the radius of gyration of the cyclopentyl group binding pocket composed by W1093.28, G902.61, and I3097.36 in Figure 6.
The fluorine sits in a largely hydrophobic pocket composed of the backbones of residues 156−158.
L95 is deeply buried in a comprehensive hydrophobic pocket composed of L87, V93, L107, L109, I143, and L164 (Fig. 3a).
Our results indicate that the 5mC binding pocket is composed of residues from discrete domains and is responsible for discrimination against 5mC derivatives, and suggest that DME, ROS1, and DML3 utilize subtly different mechanisms to probe the DNA duplex for cytosine modifications.
No conventional ATP-binding pocket, usually composed of an alpha-helix and beta-sheet mix22, was found in either KpBest or cBest1.
The X-ray structure of GSK3 β AxinGID served as a guide for orienting WWOX388−407 in the GSK3 β-binding pocket, which was composed of an α-helix, G262-L273, and an extended loop from N285 to H299.
Notably, protecting amine groups did not affect biotin avidin binding, which may be attributed to a unique conformation of biotin binding site composed of a conserved Trp120, a hydrophobic pocket, and eight hydrogen bonds, while lacking exposed amines.
