MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3103, See in JSmolClick on the image to toggle views Site type: Pout·Rout·4Bout Schematic drawing for Pout·Rout·4Bout List of all 12 Mg2+ binding sites with the site type Pout·Rout·4Bout 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 1

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3df2 B3103 Pout·Rout·4Bout 6   0.97   1.00   1.00 yes 3i1n A2941 Pout·Rout·4Bout 6   0.76   0.99   0.65 yes 3ofr A2941 Pout·Rout·4Bout 6   0.75   0.98   0.49 no 3orb A2940 Pout·Rout·4Bout 6   0.76   0.99   0.36 no 4bpe A5042 Pout·Rout·4Bout 6   0.75   0.99   1.00 yes 4dh9 A1904 Pout·Rout·4Bout 4   0.49   0.97   0.91 no 4duz A1751 Pout·Rout·4Bout 4   0.64   0.66   0.44 no 4gar A3036 Pout·Rout·4Bout 6   0.75   1.00   0.98 yes 4kj9 A3037 Pout·Rout·4Bout 5   0.88   0.32   0.21 no 4nvx A3416 Pout·Rout·4Bout 2   0.25   0.88   0.63 no 4qcr A3680 Pout·Rout·4Bout 6   0.75   1.00   0.87 yes 4too A3061 Pout·Rout·4Bout 4   0.66   0.64   0.64 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/)
For any help please contact <dust@iwonka.med.virginia.edu>