MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbe:B3457, See in JSmolClick on the image to toggle views Site type: 2Pout·4Bout Schematic drawing for 2Pout·4Bout List of all 89 Mg2+ binding sites with the site type 2Pout·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 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dv2 A1621 2Pout·4Bout 2   0.31   0.30   0.82 no 4nvx A3633 2Pout·4Bout 3   0.37   0.65   0.79 no 4duz A1620 2Pout·4Bout 3   0.49   0.65   0.77 no 4dv2 A1765 2Pout·4Bout 4   0.63   0.65   0.44 no 4dv2 A1822 2Pout·4Bout 4   0.64   0.62   0.38 no 4dr1 A1814 2Pout·4Bout 4   0.63   0.66   0.72 yes 3v2d A3164 2Pout·4Bout 4   0.42   0.57   0.86 no 3cpw 08053 2Pout·4Bout 4   0.24   0.33   0.83 no 4gau B201 2Pout·4Bout 4   0.67   0.65   0.91 yes 4dv0 A1810 2Pout·4Bout 5   0.82   0.80   0.51 yes 3v2f A3260 2Pout·4Bout 5   0.63   0.77   0.92 yes 3v2d A3670 2Pout·4Bout 5   0.60   0.79   0.73 yes 3v27 A3527 2Pout·4Bout 5   0.63   0.81   0.81 yes 4dhc A3418 2Pout·4Bout 5   0.64   0.79   0.90 yes 4qcz A3471 2Pout·4Bout 5   0.62   0.80   0.87 yes 3ofq A3003 2Pout·4Bout 5   0.82   0.80   0.76 yes 1vt2 A3003 2Pout·4Bout 5   0.82   0.80   0.72 yes 4qcp A3379 2Pout·4Bout 5   0.63   0.81   0.98 yes 4qcn A3466 2Pout·4Bout 5   0.62   0.80   0.82 yes 2qou A1548 2Pout·4Bout 6   0.97   1.00   1.00 yes 3ofx A1537 2Pout·4Bout 6   0.75   0.99   0.68 yes 3og0 A3029 2Pout·4Bout 6   0.74   1.00   0.44 no 4tp0 A1604 2Pout·4Bout 6   0.75   1.00   0.93 yes 3i21 A1553 2Pout·4Bout 6   0.75   0.99   1.00 yes 4tpa A1622 2Pout·4Bout 6   0.74   0.99   0.78 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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