MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qal:A2136, See in JSmolClick on the image to toggle views Site type: 3Pout·Rout Schematic drawing for 3Pout·Rout List of all 101 Mg2+ binding sites with the site type 3Pout·Rout 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 3 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 3v2f A3528 3Pout·Rout 3   0.37   0.71   0.82 no 4bpe A5037 3Pout·Rout 6   0.74   1.00   0.99 yes 4bpn A5037 3Pout·Rout 6   0.74   1.00   0.99 yes 4bpn A5050 3Pout·Rout 6   0.76   0.98   1.00 yes 4dh9 A1921 3Pout·Rout 4   0.49   0.98   0.88 no 4dr2 A1676 3Pout·Rout 4   0.63   0.64   1.00 yes 4dr5 A1824 3Pout·Rout 6   0.96   0.99   0.51 yes 4dr5 A1615 3Pout·Rout 1   0.14  0   0.63 no 4dr6 A1891 3Pout·Rout 6   0.94   0.99   0.22 no 4dr6 A1821 3Pout·Rout 6   0.94   1.00   0.41 no 4dr6 A1860 3Pout·Rout 6   0.96   0.98   0.24 no 4dr7 A1824 3Pout·Rout 6   0.91   0.98   0.24 no 4dr7 A1836 3Pout·Rout 6   0.92   0.97   0.19 no 4dr7 A1867 3Pout·Rout 6   0.96   0.98   0.35 no 4duz A1810 3Pout·Rout 5   0.79   0.79   0.88 yes 4duz A1628 3Pout·Rout 4   0.66   0.63   0.70 yes 4dv0 A1787 3Pout·Rout 5   0.79   0.80   0.76 yes 4dv0 A1783 3Pout·Rout 6   0.95   0.96   0.46 no 4dv0 A1823 3Pout·Rout 5   0.80   0.79   0.73 yes 4dv0 A1681 3Pout·Rout 3   0.47   0.68   0.61 no 4dv4 A1835 3Pout·Rout 6   0.95   0.99   0.47 no 4dv4 A1824 3Pout·Rout 6   0.92   0.98   0.39 no 4dv4 A1827 3Pout·Rout 5   0.80   0.78   0.37 no 4dv5 A1817 3Pout·Rout 5   0.77   0.82   0.47 no 4dv6 A1799 3Pout·Rout 6   0.95   0.99   0.48 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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