MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2wdg:Z735, See in JSmolClick on the image to toggle views Site type: 2Or Schematic drawing for 2Or List of all 560 Mg2+ binding sites with the site type 2Or 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 3 of 23 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vvl A1648 2Or 3   0.16   0.29   0.85 no 1vvl V102 2Or 2   0.06   0.13   0.59 no 1vvm A3167 2Or 2   0.07   0.13   0.99 no 1vvo A3123 2Or 2   0.06   0.13   0.53 no 1vvo A3162 2Or 2   0.28   0.11   0.78 no 1vvp A1647 2Or 3   0.23   0.33   0.85 no 1vvp A1645 2Or 2   0.10   0.28   0.55 no 1vvr V102 2Or 2   0.29   0.09   0.35 no 1vvs A3158 2Or 2   0.17   0.17   0.09 no 1vvt A1646 2Or 3   0.16   0.40   0.52 no 1vvu A3211 2Or 2   0.11   0.14   0.15 no 1vvu A3167 2Or 2   0.06   0.13   0.17 no 1vvw A3154 2Or 2   0.08   0.07   0.26 no 1vvw A3066 2Or 2   0.20   0.49   0.21 no 1vvw A3162 2Or 2   0.22   0.11   0.70 no 1vvx A1647 2Or 3   0.14   0.30   0.98 no 1vvy A3167 2Or 2   0.06   0.12   0.25 no 1vvz X102 2Or 3  0   0.41   0.57 no 1vw0 A3161 2Or 2   0.16   0.04   0.06 no 1vw0 A3123 2Or 2   0.16   0.14   0.37 no 1vx8 A1647 2Or 2   0.12   0.15   0.95 no 1vx9 A3168 2Or 2   0.05   0.11   0.87 no 1vx9 A3174 2Or 2   0.14   0.27   0.70 no 1vxj A3160 2Or 2   0.15   0.21   0.60 no 1vxj A3122 2Or 2   0.05   0.12   0.41 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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