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 14 of 67 | « Previous | Next » | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3pyr A3150 2Ob 2   0.04   0.18   0.78 no 3kiq a497 2Ob 2   0.04   0.21   0.61 no 4dr2 A1796 2Ob 2   0.04   0.21   0.98 no 2uuc Z1072 2Ob 2   0.04   0.20   0.84 no 3pyo A2970 2Ob 2   0.04   0.21   0.78 no 4b3s A2545 2Ob 2   0.04   0.17   0.79 no 4nvw A3010 2Ob 2   0.04   0.24   0.53 no 3t1y A1736 2Ob 2   0.04   0.14   0.19 no 3v2f A3080 2Ob 2   0.04   0.20   0.96 no 3knm A3115 2Ob 2   0.04   0.19   0.37 no 4duy A1737 2Ob 2   0.04   0.85   0.73 no 3t1h A1698 2Ob 2   0.04   0.18   0.03 no 3sgf A3033 2Ob 2   0.04   0.15   0.80 no 3uz6 A2268 2Ob 2   0.04   0.17   0.80 no 4l6j A5081 2Ob 2   0.04   0.18   0.75 no 4lf6 A1611 2Ob 2   0.04   0.20   0.69 no 4l6j A4798 2Ob 2   0.04   0.14   0.60 no 4ji7 A1755 2Ob 2   0.04   0.15   0.74 no 4l6j A4942 2Ob 2   0.04   0.16   0.75 no 4tp5 A3174 2Ob 2   0.04   0.18   0.61 no 4dv0 A1707 2Ob 2   0.04   0.24   0.63 no 4dr2 A1911 2Ob 2   0.04   0.27   0.78 no 3f1g A5207 2Ob 2   0.04   0.21   0.56 no 3d5d A3471 2Ob 2   0.04   0.14   0.52 no 3hux A163 2Ob 2   0.04   0.22   0.49 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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