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) [6]. ^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

1^st-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 [25]; 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).

Dudev et al. BMC Bioinformatics 2007 8:106   doi:10.1186/1471-2105-8-106