MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df3:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·3Bout Schematic drawing for 2Pout·3Bout List of all 277 Mg2+ binding sites with the site type 2Pout·3Bout 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 9 of 12 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4tov A3094 2Pout·3Bout 6   0.74   0.98   0.82 yes 4pea A1606 2Pout·3Bout 6   0.74   0.99   0.86 yes 4ton A1608 2Pout·3Bout 6   0.74   0.99   0.69 yes 3i1p A3034 2Pout·3Bout 6   0.73   0.98   0.44 no 3r8s A2996 2Pout·3Bout 6   0.73   0.99   1.00 yes 3og0 A3031 2Pout·3Bout 6   0.73   0.98   0.46 no 3ofd A3033 2Pout·3Bout 6   0.73   0.98   0.34 no 3oas A3032 2Pout·3Bout 6   0.73   0.97   0.40 no 4tol A1602 2Pout·3Bout 6   0.73   0.98   0.53 yes 4tp5 A3085 2Pout·3Bout 6   0.73   0.96   0.25 no 4tow A1608 2Pout·3Bout 6   0.73   0.98   0.76 yes 4dhb A1809 2Pout·3Bout 6   0.73   0.99   0.86 yes 3v27 A3423 2Pout·3Bout 6   0.72   0.97   0.88 yes 1nuj B419 2Pout·3Bout 6   0.72   0.88   0.82 yes 3v29 A3433 2Pout·3Bout 6   0.72   0.98   0.74 yes 3r8t A2995 2Pout·3Bout 6   0.72   0.98   1.00 yes 2nz4 Q9007 2Pout·3Bout 6   0.71   0.65   0.92 yes 3r8t A3036 2Pout·3Bout 6   0.71   0.99   0.99 yes 1nuv B412 2Pout·3Bout 6   0.70   0.80   0.93 yes 1nuj H422 2Pout·3Bout 6   0.70   0.89   0.93 yes 1m1k A8071 2Pout·3Bout 6   0.69   0.72   0.66 yes 3v2d A3554 2Pout·3Bout 6   0.69   0.94   0.70 yes 1q82 A8071 2Pout·3Bout 6   0.68   0.76   0.53 yes 1nji A8071 2Pout·3Bout 6   0.67   0.91   0.67 yes 1yij 08071 2Pout·3Bout 6   0.64   0.80   0.90 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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