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It is unlikely that Ltv1 directly interacts with Nob1, Dim1 and Rps14 in a late 43S particle that resembles mature ribosomes, as their binding sites (when based on the mature structure) are well corroborated and too distant from each other.
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The likelihood is calculated based on the time-dependent conditional probability of having exactly n binding sites when t generations before the binding site number was n0 (Wagner et al. 2007).
We found that promoters with nine binding sites expressed GFP at higher levels than promoters with three binding sites when induced, whereas increasing the spacing between binding sites did not significantly improve levels of expression (Fig. 3). Figure 3: Optimization of ZF-binding sites (triangles) in the minimal promoter for estradiol-inducible expression.
However, examination of the sequence of S. islandicus oriC2 reveals that one of the characterized mini origin recognition box (mORB) Orc1-1 binding sites has several base substitutions in conserved positions in the binding site when compared with S. solfataricus oriC2.
This region also contained a pair of 28-base inverted repeats, which form a transcription factor binding site when coiled (2327117.2327142, 2327719.2327745 [13].
However, the C- terminal exhibited much higher affinity for a cooperatively influenced binding site (for a Ca2+ binding site when the neighbouring site is occupied).
A CTCF binding site was considered a constitutive binding site when the same motif site was present in more than 90% of the 55 cell lines.
In KR2, the imino group of the Schiff base that connects the retinal with Lys255 plugs the potential Na+-binding site when KR2 is in the ground state [ 39– 41] (Fig. 1e).
Interestingly, a recent analysis based on zebrafish VDRα36 demonstrated that VDR also presents an alternative-binding site when co-crystalized with the agonist lithocholic acid.
In this study the search for HuR binding sites was based on this motif.
Thirty-two of the fifty enzymes exhibited some differences in the acceptor-binding site when compared to TM0415 (Supplementary Table 2).
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