Peaks for residues at known RING binding sites are shown: I6 in helix 1, K63 in loop 4, L97 in loop 7; C85 is the active site Cys; I88 undergoes allosteric changes upon RING binding; L103 is present in helix 2.(C) Combined 1H and 15N chemical shift perturbations of 0.18 mM 15N-UbcH5a at 0.9 molar equivalents of RNF125stop129.
The 3D patterns corresponding to the quercetin binding sites are shown in green.
The 3D patterns whose residues are located near of the quercetin and imidazole binding sites, are shown in pink.
Conserved binding site clusters associated with each protein target are represented by gray bands on the inner circle; links describing the structural similarity between two binding sites are shown in the center.
The DNA binding sites are indicated with black triangles (R35, T44, R45, T46, T47, R49 and 65H) (Xu et al., 2001), the ligand binding sites are shown with grey triangles (216G, 219S and 223W) (van Aalten et al., 2001), and the newly-proposed amino acids essential for DNA binding activity of FadR protein are highlighted with dark arrows (W60, F74 and W75).
Comparative analysis of both the human and mouse L1 promoters containing putative RUNX3 and YY1 binding sites are shown in Figure 4A and 4B.
The TSPO binding sites were shown to be widespread and with high density in several subcortical nuclei, with more moderate binding in the cortex and dorsal striatum.
In addition, their binding sites were shown to be diverse considering their size (i.e., the total number of heavy atoms in the cavity), their hydrophobicity (represented by the fraction of carbon atoms, FCA, in the cavity) and their exposure to the solvent (Additional file 1: Fig. S1).
Weak binding sites were shown to contribute significantly to TF binding [23], [34], making a binary demarcation of sites and non-sites more problematic.
