The docking predictions performed for ANTR1 indicated a distinct binding position for Pi and glutamate in the transportation cavity, at the level of Arg-120 and Arg-201, respectively.
In the following, we summarize our studies aimed at (a) elucidating the binding position for Mg2 + in the active site pocket of FTase, (b) understanding how the gap between FPP and the zinc-bound cysteine is overcome via conformational changes, and (c) the nature of the FTase prenylation transition state.
The best binding position for Pi was found to be located about 6 Å up from the bottom of the cavity, close to residue Arg-120.
The region V beta (VβV) has been identified as the binding position for superantigens and is located in the variable part of the beta chain of the TCR.
In contrast, the best binding positions for CaE were clustered rather far from the active site at the top of the gorge.
In line with that, several miRNAs were predicted for binding to the same positions of 3´-UTR SERCA2 (7 predicted miRNAs binding positions for SERCA2a, and 9 predicted miRNAs binding positions for SERCA2b), and for the majority of the predicted miRNAs there was more than one putative binding site.
The binding positions for three chemically distinct allosteric modulator classes vary along the interface but invariably increase the number of contacts that bridge the dimer.
DNA-dependent protein kinase will have different binding positions for double-stranded DNA and phosphorothioate oligodeoxycytidine 36-mer because they were not competitive in DNA-dependent protein kinase activation.
If such a 3-dimensional structure is available, PepSite analyses the SLiM-binding domain for the likely binding position of the peptide, producing a putative binary complex and a score for the likelihood of the interaction.
Therefore, we suggest that for tri-alanine to be transported across the membrane, it is likely to undergo a change in its vertical binding position, to allow for closure of the transporter.
