Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites

BMC Bioinformatics

Table 2 1^st-shell structural motifs in Mg²⁺-proteins

Motif ^a	PDB code	Mg ²⁺ -Ligands	CATH number ^b	Functional Group ^c	EC code ^d
e(24–47)h(24)k	1SJC	D¹⁸⁹, E²¹⁴, D²³⁹	3.20.20.120	Lyase^e, Isomerase^f	-
	1TKK	D¹⁹¹, E²¹⁹, D²⁴⁴	3.20.20.120	Isomerase^f	-
	2AKZ	D²⁴⁴, E²⁹², D³¹⁷	-	Lyase^e	4.2.1.11
f(1)h(109–349)b	1O08	D¹⁰⁰⁸, D¹⁰¹⁰, D¹¹⁷⁰	3.40.50.1000	Isomerase^f	5.4.2.6
	1U7P	D¹¹, D¹³, D¹²³	NYC	Hydrolase^g	-
	1WPG	D³⁵¹, T³⁵³, D⁷⁰³	3.40.50.1000	Hydrolase^g	3.6.3.8
	2B82	D⁴⁴, D⁴⁶, D¹⁶⁷	3.40.50.1000	Hydrolase^g	3.1.3.2
	2C4N	D⁹, D¹¹, D²⁰¹	NYC	Hydrolase^g	-
f(2)h(126–158)m	1KA1	D¹⁴², D¹⁴⁵, D²⁹⁴	3.30.540.10	Hydrolase^g	3.1.3.7
	1NUY	D¹¹¹⁸, D¹¹²¹, E¹²⁸⁰	3.30.540.10+ 3.40.190.80	Hydrolase^g	3.1.3.11
	2BJI	E¹⁰⁹⁰, D¹⁰⁹³, D¹²²⁰	3.30.540.10+ 3.40.190.80	Hydrolase^g	3.1.3.25
k(26–29)h(1)a	1ITZ	D¹⁶⁸, N¹⁹⁸, I²⁰⁰	3.40.50.970	Transferase^h	2.2.1.1
	1POX	D⁴⁴⁷, N⁴⁷⁴, Q⁴⁷⁶	3.40.50.970+ 3.40.50.1220	Oxidoreductaseⁱ	1.2.3.3
	1UMD	D¹⁷⁵, N²⁰⁴, Y²⁰⁶	3.40.50.970	Oxidoreductaseⁱ	1.2.4.4
	1ZPD	D⁴⁴⁰, N⁴⁶⁷, G⁴⁶⁹	3.40.50.970	Lyase^e	4.1.1.1
	2C3M	D⁹⁶³, T⁹⁹¹, V⁹⁹³	3.40.50.970	Oxidoreductaseⁱ	1.2.7.1

^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).

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