This observation is consistent with the fact that the primary binding site in GalMBP binds galactose and not fucose (Iobst and Drickamer 1994), so although both native MBP and GalMBP can bind the Lewisx structure, they must do so in very different ways, with fucose in the primary binding site of MBP and galactose in the primary binding site of GalMBP.
These are delineated as outward-facing and inward-facing, respectively, and when the extracellular substrate binds to its primary binding site termed S1, alongside Na+ and Cl−, this results in a conformational change from outward-facing to inward-facing (Yamashita et al., 2005; Kniazeff et al., 2008; Shan et al., 2011).
Structural and mutagenesis studies indicate that GalNAc and galactose bind in the primary binding site on the CRD, ligated to the binding site calcium ion and packing against a tryptophan residue for increased affinity and specificity, with further selectivity for GalNAc resulting from favorable contacts with the 2-acetamido group (Iobst and Drickamer 1996; Kolatkar et al. 1998).
Using an assay comprised of 200 nM APTS MT and 1 µM ConA, the fluorescence anisotropy capably tracks the concentration of monosaccharides that are known to bind to ConA's primary binding site, and the assay displays a MARD of 6.5% across physiologically relevant glucose concentrations.
The NMR titration data for both ZF2 and ZF3 indicate that VAImin RNA binds two zinc finger domains at saturation through a primary binding site with a relatively high affinity and a secondary binding site with a lower affinity.
Restriction of the search to a primary binding site requires knowledge of its location and also neglects multiple sites such as allosteric ones [7, 8].
We show that the primary binding site for ThT is along a shallow groove formed by adjacent Tyr and Leu residues on the β-sheet surface.
The product-ion spectra of the four fragments reveal that Met65 is the primary binding site of cisplatin on cytochrome c.
In BD, previous knowledge and restriction of the search to a primary binding site are not necessary, and therefore, it can be used in search of multiple binding sites, as well.
We present here crystal structures of IGF-I bound to such a hybrid primary binding site and of a ligand-free version of an IR αCT peptide bound to an IR L1 plus cysteine-rich domain construct (IR310.T).
To locate the primary binding site of cisplatin, both free cytochrome c and the cytochrome c adducts underwent trypsin digestion, followed by Fourier transform mass spectrometry (FT-MS) to identify unique fragments in the adduct digest.
