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We have experimentally mimicked starting points in this process by introducing primitive iron and oxygen binding sites at various locations in thioredoxin, a small protein lacking metal centers, by using computational design.
The other break point in the area around the −10 region was less restrictive because the region downstream of −10 can accommodate TR binding sites at various positions.
This suggests that the regulatory unit of a gene involves multiple transcription factor binding sites at various positions and that the spatial organization of the unit is important to bring via DNA looping at least one activated nuclear receptor protein close to the transcription start site of the respective primary nuclear receptor target gene.
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Similar to Bapx1, most of the binding sites were located distal to the TSS, with only ~ 10% (359) of the Sox9 binding sites at the TSS of various genes and 66% (2470) of the binding sites more than 25 kb distal to the TSS.
Number of genome-wide or candidate TFAP2A-modulated human protein-coding genes containing at least one or two high score TFAP2A binding sites defined at various score thresholds (10%, 20 %, 30) in their core promoters.
To validate microarray data among these 161 Klf5 putative primary targets, we selected 60 genes where Klf5 binding sites are at various distances from gene boundaries.
For the multiple binding sites system, Zhang et al. proposed a multiple binding sites equation that could calculate the binding constant and the number of binding sites at the same time [127].
Analyses of citrate binding sites on the PFK1 enzymes of various eukaryotic organisms revealed that identical amino acid residues were found at the N-terminus in all examined species (Fig. 1A); however, more variance was observed among the binding sites at the C-terminus.
a, 2mFo−DFc electron density map (blue mesh) of residues around the methylguanidinium binding site at 1σ. b, Overlay of guanidinium binding site (green) and methylguanidinium binding site (orange).
One binding site is the phosphate binding site at the catalytic cysteine residue.
(b) The substrate binding site at the subunit interface of apo-MccB.
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