MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbe:B3457, See in JSmolClick on the image to toggle views Site type: 2Pout·4Bout Schematic drawing for 2Pout·4Bout List of all 89 Mg2+ binding sites with the site type 2Pout·4Bout in RNA crystal structures in the full dataset (switch to benchmark dataset) Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv #", "Qs #", "Qe #", "PDB ID" or "Mg2+ ID" Page 1 of 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vq7 08071 2Pout·4Bout 6   0.49   0.75   0.81 no 1vs6 B2922 2Pout·4Bout 6   0.97   0.99   1.00 yes 1vs8 B2930 2Pout·4Bout 6   0.97   0.99   1.00 yes 1vt2 A3003 2Pout·4Bout 5   0.82   0.80   0.72 yes 2i2t B3016 2Pout·4Bout 6   0.97   1.00   1.00 yes 2otj 08071 2Pout·4Bout 6   0.79   0.69   0.99 yes 2qal A2031 2Pout·4Bout 6   0.97   0.99   1.00 yes 2qam B3457 2Pout·4Bout 6   0.97   0.99   1.00 yes 2qao B3152 2Pout·4Bout 6   0.97   0.99   1.00 yes 2qb9 A2031 2Pout·4Bout 6   0.97   1.00   1.00 yes 2qba B3457 2Pout·4Bout 6   0.97   0.99   1.00 yes 2qbc B3152 2Pout·4Bout 6   0.97   0.99   1.00 yes 2qbe B3457 2Pout·4Bout 6   0.97   1.00   1.00 yes 2qbh A1548 2Pout·4Bout 6   0.97   1.00   1.00 yes 2qbk B2930 2Pout·4Bout 6   0.97   1.00   1.00 yes 2qou A1548 2Pout·4Bout 6   0.97   1.00   1.00 yes 2xzm 014 2Pout·4Bout 6   0.12   0.99   1.00 no 2xzn 034 2Pout·4Bout 6   0.11   0.99   1.00 no 2xzn 014 2Pout·4Bout 6   0.12   0.99   1.00 no 3cc2 08071 2Pout·4Bout 6   0.73   0.94   0.67 yes 3cpw 08053 2Pout·4Bout 4   0.24   0.33   0.83 no 3i1n A2974 2Pout·4Bout 6   0.75   0.98   0.40 no 3i1p A2980 2Pout·4Bout 6   0.74   0.99   0.58 yes 3i1t A2978 2Pout·4Bout 6   0.74   1.00   1.00 yes 3i20 A2974 2Pout·4Bout 6   0.74   0.99   1.00 yes

^# Validation parameters Q_v, Q_s, Q_e are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Q_v measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg²⁺ (+2)
Q_s measures the geometrical symmetry of the ligands distribution around the Mg²⁺ required for octahedral geometry
Q_e measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg²⁺ compared to those of all atoms in its environment

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

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