MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·2Bout Schematic drawing for 2Pout·2Bout List of all 453 Mg2+ binding sites with the site type 2Pout·2Bout 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 19 | « 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 3v23 A3369 2Pout·2Bout 5   0.63   0.81   0.92 yes 4dv0 A1763 2Pout·2Bout 4   0.63   0.66   0.58 yes 4nvx A3373 2Pout·2Bout 5   0.63   0.77   0.78 yes 3ox0 B124 2Pout·2Bout 5   0.63   0.81   0.75 yes 4qcu A3163 2Pout·2Bout 5   0.63   0.80   0.94 yes 4qcp A3399 2Pout·2Bout 5   0.62   0.80   0.88 yes 4ji2 A1806 2Pout·2Bout 4   0.62   0.64   0.37 no 4dha A3566 2Pout·2Bout 5   0.62   0.80   0.95 yes 3v2f A3386 2Pout·2Bout 5   0.62   0.80   0.79 yes 4ji4 A1793 2Pout·2Bout 4   0.62   0.64   0.38 no 3v25 A3303 2Pout·2Bout 5   0.62   0.79   0.96 yes 3v2e A1690 2Pout·2Bout 5   0.62   0.77   0.77 yes 1yjn 08100 2Pout·2Bout 6   0.62   0.62   0.74 yes 4dha A3665 2Pout·2Bout 5   0.61   0.78   0.75 yes 3v23 A3365 2Pout·2Bout 5   0.61   0.79   0.94 yes 4dv1 A1828 2Pout·2Bout 4   0.61   0.69   0.33 no 3v2f A3482 2Pout·2Bout 5   0.61   0.76   0.63 yes 3dil A229 2Pout·2Bout 5   0.58   0.84   0.98 yes 4dr1 A1638 2Pout·2Bout 3   0.55   0.63   0.87 no 4dha A3529 2Pout·2Bout 4   0.54   0.59   0.66 no 3v24 A1669 2Pout·2Bout 4   0.52   0.98   0.90 yes 4dv4 A1632 2Pout·2Bout 3   0.52   0.66   0.89 no 4nvx A3321 2Pout·2Bout 4   0.51   0.62   0.90 yes 3v29 A3353 2Pout·2Bout 4   0.51   0.97   0.89 yes 4nvv A3518 2Pout·2Bout 4   0.51   0.62   0.94 yes

^# 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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