To test this hypothesis, we compared the binding sites of a mutant KAP1 with no RBCC domain (mt KAP1) versus the binding sites of wild-type KAP1 (wt KAP1) on HEK293 cells (see Materials and Methods section).
Masitinib was docked into the ATP-binding site of wild-type KIT and ABL using the coordinates of human KIT and ABL in the inactive conformation.
After manual adjustment, the final monomer structure was refined with one full occupancy molecule of DRV oriented approximately perpendicular to DRV in the typical inhibitor-binding site of wild-type PR or most mutants, as indicated by the clear electron density map.
The contribution of the + 3 subsite to the substrate specificity of BsXynA was established more in detail by mapping the enzyme binding site of the wild type xylanase and mutant Y88A with labelled xylo-oligosaccharides.
However, because of its small size, 5HFA resides loosely in the binding site of the wild type enzyme (Additional file 7C), which explains its low affinity and reduced turnover of 5HFA compared with tricetin.
Prior results showed that either ADP or ATP could bind to the nucleotide binding site of PII and that wild-type heterotrimers could sense the ratio of ATP to ADP, a reflection of the adenylate energy charge (10).
We postulated that by using an inactive mutant CTB protein as the scaffold, once modified with carbohydrates, the resulting pentavalent ligand should provide a precise fit of the ligand groups with the spacing and configuration of binding sites on wild-type CTB.
For example, the preferred in vitro binding site of AtERF1, AtERF2 and AtERF5 is the wild type GCC box, AGCCGCC [ 25].
Single amino acid mutations were introduced to the HBGA binding site of the P protein of BV through site-directed mutagenesis using the wild type construct of P domain (in plasmid pGEX-4T-1, GE Heastemplateife Sciences) as template.
The reporter plasmids consisted of either three copies of a wild-type consensus binding site for AR, or three copies of a mutated binding site of AR conjugated to a firefly luciferase reporter.
