MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2avy:A1578, See in JSmolClick on the image to toggle views Site type: Pout·Rout Schematic drawing for Pout·Rout List of all 142 Mg2+ binding sites with the site type Pout·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 2 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dv1 A1648 Pout·Rout 4   0.62   0.65   0.66 yes 4ji2 A1648 Pout·Rout 3   0.47   0.70   0.66 no 4dr3 A1649 Pout·Rout 3   0.48   0.66   0.97 no 4dr6 A1649 Pout·Rout 3   0.48   0.67   0.95 no 4dr4 A1690 Pout·Rout 2   0.31   0.31   0.99 no 4dv1 A1696 Pout·Rout 2   0.31   0.29   0.81 no 4dr2 A1731 Pout·Rout 4   0.63   0.65   1.00 yes 4dr2 A1749 Pout·Rout 5   0.79   0.80   1.00 yes 3v2c A1749 Pout·Rout 3   0.37   0.44   0.93 no 4dr4 A1752 Pout·Rout 5   0.77   0.79   0.99 yes 3v28 A1754 Pout·Rout 5   0.62   0.80   0.96 yes 4qcm A1765 Pout·Rout 1   0.12  0   0.89 no 4dv1 A1766 Pout·Rout 5   0.80   0.80   0.70 yes 4ji6 A1773 Pout·Rout 6   0.88   1.00   0.24 no 4qcm A1779 Pout·Rout 3   0.38   0.42   0.93 no 4dv6 A1792 Pout·Rout 4   0.63   0.64   0.36 no 4ji6 A1796 Pout·Rout 6   0.88   0.97   0.37 no 4ji8 A1801 Pout·Rout 6   0.87   0.98   0.32 no 4dr5 A1805 Pout·Rout 6   0.96   0.99   0.54 yes 4nxn A1808 Pout·Rout 5   0.80   0.80   0.57 yes 4ji8 A1810 Pout·Rout 6   0.90   0.96   0.31 no 4dr7 A1816 Pout·Rout 6   0.91   0.98   0.29 no 4dr5 A1818 Pout·Rout 6   0.95   1.00   0.43 no 4dr6 A1822 Pout·Rout 6   0.95   1.00   0.43 no 4ji6 A1823 Pout·Rout 6   0.89   0.96   0.20 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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