MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3v6u:A1653, See in JSmolClick on the image to toggle views Site type: 2Or·Nb Schematic drawing for 2Or·Nb List of all 122 Mg2+ binding sites with the site type 2Or·Nb 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 5 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 3v6u A1653 2Or·Nb 4   0.84   0.76   0.89 yes 4dh9 A1809 2Or·Nb 3   0.08   0.54   0.89 no 4dha A3046 2Or·Nb 3   0.12   0.68   0.80 no 4dv7 A1854 2Or·Nb 3   0.05   0.70   0.75 no 4hub 08108 2Or·Nb 3   0.19   0.41   0.85 no 4kfh A2442 2Or·Nb 3   0.06   0.57   0.53 no 4kfh A2034 2Or·Nb 4   0.15   0.68   0.79 no 4l6j A6081 2Or·Nb 4   0.12   0.90   0.52 no 4l6j A5913 2Or·Nb 3   0.07   0.48   0.69 no 4mgm B102 2Or·Nb 3   0.10   0.39   0.80 no 4nvx A3037 2Or·Nb 4   0.07   0.68   0.99 no 4nvz A3266 2Or·Nb 3   0.09   0.36   0.43 no 4nw1 A3164 2Or·Nb 3   0.08   0.20   1.00 no 4qcn A3001 2Or·Nb 3   0.11   0.52   0.83 no 4qcn A3256 2Or·Nb 4   0.09   0.64   0.83 no 4qct A3165 2Or·Nb 3   0.16   0.22   0.96 no 4qcv A3648 2Or·Nb 4   0.17   0.40   0.82 no 4qcv A3584 2Or·Nb 4   0.18   0.39   0.93 no 4qcv A3002 2Or·Nb 3   0.11   0.63   0.67 no 4qcx A3584 2Or·Nb 4   0.17   0.43   0.93 no 4qcz A3688 2Or·Nb 4   0.18   0.46   0.98 no 4qd1 A3155 2Or·Nb 3   0.19   0.22   0.94 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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