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NTD had been implicated before as a binding site of donor dsDNA [9], [21].
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Kinetic (Km and Vmax) and inhibition constants (Ki) were measured and reveal that almost the entire γ-glutamyl moiety is necessary for recognition in the binding site of the donor substrate.
Although, the binding sites of NAD+ donor are quite similar, the substrate acceptor sites are quite different.
Structural representation showing the binding site of the inhibitors.
(D) Comparison between adamantane binding site and HMA binding site of HCV p7 channels.
(E) Stereo view of an overlay of the conserved donor substrate binding sites of WbnH, MshA with UDP and PimA with GDP-Man.
When the binding sites of the cpAvd5→4 domains were blocked with biotin before addition of DY633-biotin, the emission of the donor was quenched less than 13% (Figure 4D).
In the phosphate-donor-binding site of PPi-PFK, two basic residues were found (e.g., K148 and H384 in PPi-PFK from Borrelia burgdorferi), which are not conserved in ATP-PFK.
Paz, I. et al. RBPmap: a web server for mapping binding sites of RNA-binding proteins.
Predicted ligand binding sites of YD1.
SiteMap characterizes the possible binding sites of a protein by analyzing several physical chemical properties, such as size, volume, exposure to solvent, hydrophobic and hydrophilic space, and H-donor/-acceptor ability [43, 44].
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