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 3cd6 08066 Pout·Rout 2   0.04   0.32   0.89 no 3cma 08078 Pout·Rout 3   0.08   0.44   0.60 no 3cpw A8050 Pout·Rout 6   0.36   0.64   0.69 no 3g4s A8050 Pout·Rout 6   0.21   0.77   1.00 no 3g78 A419 Pout·Rout 2   0.28   0.12   0.07 no 3i1p A2918 Pout·Rout 6   0.73   0.99   0.52 yes 3i1s A1570 Pout·Rout 5   0.81   0.82   1.00 yes 3i1t A2918 Pout·Rout 6   0.73   0.99   1.00 yes 3i55 A8050 Pout·Rout 6   0.18   0.79   0.75 no 3nkb B202 Pout·Rout 3   0.11   0.54   0.79 no 3ofd E202 Pout·Rout 6   0.73   0.98   0.40 no 3ofq A2919 Pout·Rout 6   0.74   0.98   0.43 no 3v23 A3106 Pout·Rout 1   0.02  0   0.99 no 3v27 A3569 Pout·Rout 4   0.48   0.95   0.81 no 3v27 A3619 Pout·Rout 6   0.72   0.97   0.93 yes 3v28 A1754 Pout·Rout 5   0.62   0.80   0.96 yes 3v2c A1642 Pout·Rout 4   0.52   0.62   0.93 yes 3v2c I201 Pout·Rout 2   0.25   0.39   0.94 no 3v2c A1749 Pout·Rout 3   0.37   0.44   0.93 no 3v2d A3577 Pout·Rout 3   0.37   0.61   0.58 no 3v2d A3609 Pout·Rout 2   0.22   0.53   0.62 no 3v2d A3652 Pout·Rout 4   0.47   0.98   0.51 no 3v2d A3695 Pout·Rout 4   0.48   0.63   0.72 no 3v2d A3569 Pout·Rout 2   0.22   0.32   0.72 no 3v2d A3427 Pout·Rout 3   0.35   0.67   0.58 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].

---

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>