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The structural motif discovery method presented herein is general and can be …
Biology Articles » Biochemistry » Protein Biochemistry » Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites » Tables
The letter and secondary structural element (SSE) frequency distributions and 2-sample T-tests of first-and second-shell amino acid residues vs. all amino acid residues in the Mg2+-proteins
a16-letter structural alphabet defined by de Brevern and co-workers (see Methods and original reference) . bThe ratio of the letter/SSE 'x' frequency of first-shell amino acid residues to that of all amino acid residues in the 70 Mg2+ proteins. cThe statistical analyses were carried out using the package, SAS/STAT version 8 (SAS Institute, NC). dP-values eThe ratio of the letter/SSE 'x' frequency of second-shell amino acid residues to that of all amino acid residues in the 70 Mg2+ proteins.
Dudev et al. BMC Bioinformatics 2007 8:106 doi:10.1186/1471-2105-8-106
1st-shell structural motifs in Mg2+-proteins
aThe number in parentheses indicates the number of residues separating the letters corresponding to the Mg2+-bound residues. bThe CATH code of the domain containing the Mg2+-ligands; a dash implies that no domain could be assigned to the PDB entry, while NYC means the protein has not yet been chopped. cThe functional group from the PDB header. dThe enzyme class from PDBsum ; a dash means no EC code was found. eLyases (EC4---) catalyze C-C/O/N and other bond cleavage; e.g., RCOCOOH → RCOH + CO2. fIsomerases (EC5---) catalyze geometric changes within a molecule. gHydrolases (EC3---) catalyze hydrolytic bond cleavage: AB + H2O → AOH + BH. hTransferases (EC2---) catalyze AB + C → A + BC. iOxidoreductases (EC1---) catalyze oxido-reductions: AH + B → A + BH (reduced) and A + O → AO (oxidized).
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