MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1egk:C14, See in JSmolClick on the image to toggle views Site type: Bout Schematic drawing for Bout List of all 988 Mg2+ binding sites with the site type Bout 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 40 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1dno B21 Bout 6   0.97   0.99   0.81 yes 1egk C14 Bout 6   0.99   0.99   1.00 yes 1egk C6 Bout 6   0.96   1.00   1.00 yes 1feu D319 Bout 2   0.21   0.23   0.82 no 1l9a B241 Bout 1   0.05  0   0.78 no 1l9a A107 Bout 2   0.33   0.05   0.94 no 1o3z A301 Bout 3   0.40   0.66   0.76 no 1tra A80 Bout 6   0.76   0.99   0.50 no 1vqo 08090 Bout 1   0.05  0   0.88 no 1vqp 08082 Bout 2   0.04   0.62   0.76 no 1vs5 A1565 Bout 6   0.97   0.99   1.00 yes 1vs5 A1569 Bout 6   0.97   1.00   1.00 yes 1vt2 A3013 Bout 3   0.50   0.43   0.61 no 1vt2 A3034 Bout 6   0.74   1.00   0.59 yes 1xp7 A103 Bout 1   0.17  0   0.73 no 1xp7 B101 Bout 1   0.26  0   0.59 no 1y39 D410 Bout 1   0.07  0   0.88 no 1y3s A25 Bout 2   0.18   0.09   0.70 no 1y73 A27 Bout 1   0.01  0   0.93 no 2avy A1567 Bout 6   0.97   0.99   0.50 yes 2avy A1564 Bout 6   0.97   0.99   1.00 yes 2b8r A101 Bout 1   0.13  0   0.78 no 2i2p A1561 Bout 5   0.81   0.80   1.00 yes 2i2t B2907 Bout 6   0.97   1.00   1.00 yes 2i2u A1589 Bout 5   0.81   0.80   1.00 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].

---

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>