Table 2. Three RNA-inner and three RNA-outer validated Mg²⁺-binding motifs previously reported in the literature (I–VI).

ID	Motif name	Reference	Systematic classification		Detailed features of the motif	Number of sites
			Class	Type
I	Magnesium Clamp	Ennifar et al. (1999) (7) Petrov et al. (2011) (30)	RNA-inner	cis-2Ophtrans-2Oph	The two Oph atoms are from distant phosphates	823 (cis)207 (trans)
II	10-member ring	Hsiao et al. (2009) (12)	RNA-inner	cis-2Oph	The two Oph atoms are from sequentially consecutive phosphates	802
				fac-3Oph mer-3Oph	The three Oph atoms are from sequentially consecutive phosphates	63 (fac) 39 (mer)
				fac-3Ophmer-3Oph	10-member ring with additional Oph atom coming from phosphate which is separated by one residue from either 10-member ring phosphates	10 (fac)74 (mer)
				4Oph	One Mg2+ coordinated by two unrelated 10-member rings	37
III	G-phosphate	Klein et al. (2004) (10)	RNA-inner	Oph•Ob	Ob atom is from guanine	250
IV	G•G metal-binding site	Correll et al. (1997) (8)	RNA-outer	2Pout•2Bout	Mg2+ is bound through the outer sphere by two sequentially consecutive guanines and by two phosphate moieties from residues n and n-1 where n is residue number of the lower guanine in the sequence.	95
		3OFA-A1569		2Bout	Mg2+ is bound through the outer sphere by two sequentially consecutive guanine moieties	374
		3V23-A3619		Pout•2Bout	Mg2+ is bound through the outer sphere by two consecutive guanines and a distant phosphate	57
V	Triple G Motif	Tinoco & Keift (1997) (2)	RNA-outer	3Bout	Mg2+ is bound through the outer sphere by three sequentially consecutive guanine bases	34
VI	Metal ion zipper	Correll et al. (1997) (8)	RNA-outer	2Pout	Mg2+ binds two distant phosphates through the outer sphere	97

The site type(s) and additional features used to define each motif are tabulated. The term ‘distant’ phosphates/residues is used to specify two phosphates or residues coming from different RNA chains or separated by more than seven residues in the same chain. The terms ‘upstream’/‘downstream’ residues are used to specify a residue lower/higher in the sequence of the same chain. Representative examples of each motif are depicted in Supplementary Figure S5.