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Active sites in Enzymes can be divided in subsides (S) which consist of single amino acids. The subsides are flanking the catalytic site [C] and are numbered starting at the catalytic site. An Enzyme with 4 subsites on the one side and 3 subsides on the other side of the catalytic site has the following nomenclature S4-S3-S2-S1-[C]-S1'-S2'-S3'
The corresponding positions (P) of the substrate have the same numbering as the subsides they occupy. The positions are counted from the point of cleavage. Note that not in all cases every subside in occupied by a aminoacid of the substrate. Thus finally the P residue describes the aminoacid or molecule which can be found at that specific location of substrate.
P4-P3-P2-P1------P1'-P2' ------ = point of cleavage
S4-S3-S2-S1-[C]-S1'-S2'-S3'
Reference: Schechter and Berger (1967) On the size of active sites in proteases (Biochem. Biophys. Res. Commun. 27, 157-162
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