Among many other binding sites lost in the –673 construct were an E-box, a STAT binding site which forms a sequence model (Genomatix modelInspector) together with an ets binding site, and a Myc associated zinc finger binding site (MAZF).
This action substantially perturbs the magnesium binding site, which is primarily formed by T92.
Amongst these, the BC and FG loops in hTIM-1 form an unique groove-like structure adjacent to the PS binding site, which is in-turn formed by FG and CC' loops (Figs. 3C and 4).
The linear dependence of the rate of its conversion on Na+ concentration indicates that entry of Na+ into a transiently formed binding site, which arises during the photocycle, becomes rate-limiting.
It has several binding sites on each fibrinogen-like domain: an outer binding pocket, also present in H-and M-ficolins, together with three unique sites, which form a continuous binding surface for various acetylated and neutral carbohydrate ligands.
It bears a very peculiar network of interactions at the binding site, which revolves around the coordination complex formed by a zinc ion, three hystidine residues, and the inhibitor.
In BMP-2 the helix is formed because the highly concave site of the wrist epitope forms a 120° spanning binding site, which is usually seen in structural arrangements of amphipathic helix/helices (e.g. hydrophobic cores in helical bundles).
When binding to DNA, LysR protein forms a homodimer and targets two specific binding sites, a regulatory binding site, which has the conserved T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAAig. 2b).
The specificity of these protein-DNA complexes for B-Myb was further verified by an oligonucleotide cassette containing base pair changes within the putative MYB-binding site, which failed to form DNA complexes in either R1 or HeLa cells, and by addition of a 200-fold molar excess of unlabeled competitor oligonucleotide.
PRL contains two receptor binding sites which sequentially interact with two PRLR molecules to form a ternary complex.
