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One of the most frequent categories (189 CgrA binding sites) involves a CgrA binding site mapped uniquely to an intergenic region located just upstream of a gene (Fig. 3B).
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This is likely due to the fact that the interactions in the respective binding sites involve a lot of specific hydrogen bonds and salt bridges with the ligands (Fig. 2).
Other methods for identifying antibody binding sites involve: (a) proteolysis of the antigen, (b) recombinant techniques, (c) phage display, (d) mass spectrometry and (e) the use of synthetic peptides.
At least with respect to the binding sites involving the G domain, H-Ras is an excellent model for K-Ras and probably N-Ras as well.
Thirdly, the possibility exists that Ets binding sites involved in the regulation of these genes are located within a region outside of the 1000 base pairs searched in our study.
A somewhat surprising finding was that the ion binding sites involve the backbone carbonyl groups of the amino acids rather than their side chains.
Most binding sites involve interaction with the 3- and 4-hydroxyl groups and bind selectively either to mannose-type sugars, including mannose, glucose and GlcNAc, or to galactose-type sugars, including galactose and GalNAc (Weis and Drickamer 1996).
Therefore, a promising strategy of hybridizing two pharmacophores that target distinct binding sites involved in pain modulation and transmission was established.
However, the H+ or Ca2+ binding sites involved in gating and the gating mechanism are not fully known.
Three main sites (S1 S3) are located in the protein active site; S1 and S2 overlap with the phosphate binding sites involved in RNase nucleotide recognition.
We conclude that these two CaM binding sites, the high-affinity 1-8-14 CaM bindomainomain in the N-terminus and the previously described C-terminal binding domain at AA 707-276, are the major binding sites involved in CaM binding to EAG1.
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