Table 3. Seven newly discovered and validated Mg²⁺-binding motifs.

ID	Motif name	Representative site	Systematic classification		Detailed features of the motif	Number of sites
			Class	Type
A	Y-clamp	2Z75-B301	RNA-inner	mer-3Oph	10-member ring and one distant Oph atom in mer- conformation	279
B	U-phosphate	2YIE-Z1116	RNA-inner	Oph•Ob	Ob atom is from uracil	199
C	12-member ring	2AVY- A1566	RNA-outer	2Pout	Mg2+ is bound through the outer sphere by two sequentially consecutive phosphates forming a ring with 12 non-hydrogen atoms	82
D	Purine-N7 seat	2QBA-B3321	RNA-inner	2Nb	Mg2+ is bound by two guanine or adenine N7 atoms in inner sphere and capped by 3 or 4 downstream phosphates through the outer sphere	141
E	G-N7 macro-chelate I	3V29-A3359	RNA-inner	Nb•Pout	Mg2+ is bound by guanine N7 atom in inner sphere and phosphate of the same residue in the outer sphere	60
F	G-N7 macro-chelate II	2AW7-A1569	RNA-outer	Pout•Bout	Mg2+ is bound through the outer sphere by guanine N7 atom and phosphate of the same residue	18
G	10-member ring with purine-N7	3V23-A3540	RNA-inner	2Oph•Nb	10-member ring with N7 atom of purine base which is separated by one residue from either of the 10-member ring phosphates	45

The PDB accession codes with the residue number for the magnesium ion are shown for representative sites of each motif (as depicted in Figure 6). Site type and additional features used to define each motif are tabulated.