MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2r8s:R1004, See in JSmolClick on the image to toggle views Site type: 2Ob Schematic drawing for 2Ob List of all 1662 Mg2+ binding sites with the site type 2Ob 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 11 of 67 | « Previous | Next » | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3cxc 08042 2Ob 6   0.21   0.63   0.87 no 3u56 B2207 2Ob 5   0.21   0.81   0.51 no 3cd6 08076 2Ob 6   0.21   0.73   0.96 no 4ji2 A1652 2Ob 3   0.21   0.28   0.82 no 3g6e 08075 2Ob 6   0.21   0.83   0.88 no 3ccv 08032 2Ob 6   0.20   0.82   0.76 no 3ccj 08032 2Ob 6   0.20   0.77   0.95 no 2wdh Z191 2Ob 2   0.20   0.06   0.87 no 1yjn 08042 2Ob 6   0.20   0.86   0.82 no 4ji7 A1641 2Ob 3   0.20   0.18   0.43 no 3kiq a1620 2Ob 2   0.20   0.06   0.42 no 4dr3 A1717 2Ob 3   0.20   0.17   0.89 no 4dv5 A1697 2Ob 3   0.20   0.24   0.87 no 4nxn A1708 2Ob 3   0.20   0.14   0.96 no 4ji0 A1768 2Ob 2   0.20   0.09   0.97 no 4gkj A1640 2Ob 2   0.20   0.40   0.99 no 2wdg Z161 2Ob 2   0.20   0.29   0.48 no 1vvu A3158 2Ob 2   0.19   0.11   0.30 no 4ji0 A1630 2Ob 3   0.19   0.19   0.95 no 4dv3 A1693 2Ob 3   0.19   0.18   0.77 no 4gkk A1641 2Ob 2   0.19   0.25   1.00 no 3t1y A1641 2Ob 2   0.19   0.25   0.32 no 2vqf Z2 2Ob 2   0.19   0.19   0.82 no 2xfz Z291 2Ob 2   0.19   0.28   0.57 no 4qcr A3786 2Ob 4   0.19   0.28   0.69 no

^# 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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