MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 4g5m:A1746, See in JSmolClick on the image to toggle views Site type: Ob·2Nb Schematic drawing for Ob·2Nb List of all 105 Mg2+ binding sites with the site type Ob·2Nb 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 4 of 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4qco A3072 Ob·2Nb 3   0.08   0.21   0.85 no 1i94 A1555 Ob·2Nb 3   0.14   0.24   0.85 no 3fs0 B140 Ob·2Nb 4   0.06   0.52   0.85 no 1vvz A1670 Ob·2Nb 3   0.52   0.27   0.86 no 4tp2 A1646 Ob·2Nb 3   0.27   0.49   0.86 no 1i95 A1558 Ob·2Nb 3   0.10   0.30   0.86 no 4kix A3020 Ob·2Nb 5   0.64   0.49   0.86 no 3i9d A1719 Ob·2Nb 3   0.35   0.28   0.87 no 4ji8 A1720 Ob·2Nb 4   0.51   0.27   0.87 no 1i96 A1557 Ob·2Nb 3   0.10   0.26   0.87 no 4tzz F203 Ob·2Nb 3   0.33   0.41   0.89 no 4qcr A3606 Ob·2Nb 5   0.32   0.94   0.90 no 3v6u A1630 Ob·2Nb 3   0.50   0.68   0.91 no 4nw1 A3034 Ob·2Nb 3   0.15   0.21   0.91 no 3v25 A3077 Ob·2Nb 3   0.06   0.37   0.92 no 4kx0 A3203 Ob·2Nb 3   0.63   0.26   0.92 no 3ktv A6 Ob·2Nb 3   0.07   0.22   0.93 no 4g5k A1850 Ob·2Nb 3   0.29   0.56   0.93 no 4g5m A1746 Ob·2Nb 3   0.81   0.68   0.94 no 4qcx A3274 Ob·2Nb 6   0.45   0.78   0.94 no 4kjb A3044 Ob·2Nb 4   0.26   0.38   0.95 no 3i8h A2025 Ob·2Nb 3   0.29   0.23   0.95 no 4qct A3041 Ob·2Nb 3   0.12   0.44   0.95 no 4g5t A2063 Ob·2Nb 3   0.29   0.47   0.96 no 2qus B73 Ob·2Nb 3   0.72   0.51   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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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