MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 4bpp:A5052, See in JSmolClick on the image to toggle views Site type: Rout Schematic drawing for Rout List of all 116 Mg2+ binding sites with the site type Rout 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 1 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 1k8a C8065 Rout 6   0.89   0.83   0.73 yes 1kc8 C8065 Rout 6   0.87   0.76   0.83 yes 1kd1 C8065 Rout 6   0.79   0.72   0.84 yes 1kqs A8065 Rout 6   0.78   0.91   0.97 yes 1m1k C8065 Rout 6   0.76   0.80   0.82 yes 1n8r C8065 Rout 6   0.75   0.86   0.83 yes 1q81 C8065 Rout 6   0.92   0.88   0.84 yes 1q82 C8065 Rout 6   0.73   0.76   0.87 yes 1q86 C8065 Rout 6   0.80   0.87   0.82 yes 1qvf A8065 Rout 4   0.70   0.65   0.58 yes 1qvg A8065 Rout 6   0.77   0.79   0.98 yes 1vq4 A8065 Rout 6   0.65   0.91   0.92 yes 1vq6 A8065 Rout 6   0.70   0.87   0.95 yes 1vql 08065 Rout 4   0.26   0.50   0.64 no 1vqp A8065 Rout 5   0.37   0.58   0.64 no 1w2b A1238 Rout 5   0.22   0.80   0.88 no 1yhq A8050 Rout 6   0.76   0.71   0.81 yes 1yi2 A8065 Rout 6   0.96   0.81   0.94 yes 1yjw A8065 Rout 6   0.87   0.85   0.73 yes 2gcs B506 Rout 2   0.26   0.52   0.91 no 2h0x B506 Rout 2   0.14   0.48   0.88 no 2otj A8065 Rout 6   0.65   0.66   0.83 yes 2pjp B104 Rout 2   0.12   0.33   0.69 no 2qex A8065 Rout 6   0.40   0.65   0.88 no 2qex 08024 Rout 1   0.05  0   0.74 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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