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 3 of 67 | « 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 4ji7 A1678 2Ob 2   0.03   0.16   0.68 no 4dv7 A1739 2Ob 2   0.03   0.16   0.92 no 2wdk Z173 2Ob 2   0.03   0.20   0.76 no 4nvz A3038 2Ob 2   0.03   0.23   0.61 no 4dr7 A1903 2Ob 2   0.03   0.14   0.72 no 3d5a A1784 2Ob 2   0.03   0.17   0.34 no 3oi3 A2980 2Ob 2   0.03   0.19   0.97 no 3pyo A3125 2Ob 2   0.03   0.16   0.83 no 4ji7 A1735 2Ob 2   0.03   0.17   0.64 no 2wdg Z189 2Ob 2   0.03   0.18   0.96 no 1vxt A3159 2Ob 2   0.03   0.17   0.76 no 3oh5 A3019 2Ob 2   0.03   0.18   0.63 no 3ivn A101 2Ob 2   0.03   0.17   0.91 no 3u5f 62149 2Ob 2   0.03   0.22   0.90 no 3u5b 22067 2Ob 2   0.03   0.21   0.76 no 4aqy A2695 2Ob 2   0.03   0.17   0.94 no 1vvo A3210 2Ob 2   0.03   0.21   0.98 no 3v25 A3224 2Ob 2   0.03   0.13   0.88 no 4dv2 A1734 2Ob 2   0.03   0.21   0.66 no 4dhc A3002 2Ob 2   0.03   0.20   0.50 no 1hr2 A60 2Ob 2   0.03   0.20   0.90 no 3ohc A1573 2Ob 2   0.03   0.18   0.68 no 4nvx A3031 2Ob 2   0.03   0.17   0.76 no 4qcq A3080 2Ob 2   0.03   0.22   0.75 no 3uzg A1800 2Ob 2   0.03   0.58   0.97 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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