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Reposted from Quora http://www.quora.com/What-is-the-distance-between-the-3-18s-rRNA-the-Kozak-consensus-sequence-and-the-A-site-of-eukaryotic-ribosomes-during-protein-translation

The Kozak sequence is shown to be important in translation initiation, and the A-site is the anti-codon recognition site. If the distance is not known, how could I find out what it is? Is the crystal structure of the whole mRNA-rRNA-tRNA complex determined? If so, what modeling program would be best for establishing intermolecular distances?

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to begin with you can find the distance between the kozak consensus sequence and the start codon for all genes and obtain a distribution. This can be a good estimate of actual distances... I dont know if this comment is still useful.. its been more than a year.. :P –  WYSIWYG Oct 4 '13 at 8:45

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