These sites coincide with non-specific binding sites for multiple transcription factors ('HOT' sites), which become occupied when cenH3 is lost.
Frembgen-Kesner et al. showed that cryptic drug binding sites, which appear only when the target has bound a ligand already, become more apparent over the course of MD simulations than in the original PDB structures [ 51].
The PACAP specific binding sites which were not shared VIP were termed type I, while the binding sites shared with both PACAP and VIP were termed Type II.
To generate a list of unambiguous CTCF negative RAD21 binding sites we removed these sites, leaving 667 reassessed CTCF independent RAD21 binding sites, which we define as motif and CTCF-independent RAD21 binding sites (MCIB).
The sequence of this binding site does not resemble any known ATP binding sites, which have much higher binding affinities.
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.
SMD studies of LeuT also revealed for the first time the location of a putative secondary substrate binding site, which was later verified experimentally and became a topic for much debate over its significance to the transport mechanism.
Sum1 binds a DNA binding site which resembles, and partly overlaps, the binding site of Ndt80 [ 23], [ 18].
In all of the other examples, there is a loop adjacent to the cofactor binding site which is disordered in the apo structure and which, in all but the last example, becomes ordered when the cofactor binds.
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).
