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EF-P binds to a site located between the binding site for the peptidyl tRNA (P site) and the exiting tRNA (E site).
This suggests that within the pore a gate is located between the binding site(s) for ions and the extracellular mouth of the channel.
If the target in question is a protein, high sequence similarity between the binding site and that of other proteins will make such selectivity more challenging.
The subsequent distance between the binding site and CCG was ~1.39 Å. Dominant concerted motions of G-quadruplex in both ensembles were investigated by PCA.
Because the endogenous fluorescence of protein is mainly produced by Trp residue, the distance between the binding site of the drug and the Trp residue can be calculated by the Förster's non-radiative energy transfer theory.
Database searches revealed homology between the binding site in the model and 1,4-dihydroxy-2-naphthoate octaprenyltransferases (e.g. Q17BA9_AEDAE).
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Overlap between the binding sites of Rad26 and Spt4 Spt5 on Pol II.
The identified compound exploits the subtle differences between the binding sites of Plk1 and other Ser/Thr kinases including Plk2-4.
In addition, the electrostatic potential binding energy and similarity between the binding sites can be calculated based on the binding pose of the ligand.
(A) Schematic description of the hypothetical duplexes formed by the interactions between the binding sites in the CDK6 3′-UTR (top) and miR-29b (bottom).
(C) Schematic depicting the hypothetical duplexes formed through interactions between the binding sites in the Slug 3′-UTR (top) and miR-203 (bottom).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com