MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df3:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·3Bout Schematic drawing for 2Pout·3Bout List of all 277 Mg2+ binding sites with the site type 2Pout·3Bout 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 12 | « 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 4a1e 01 2Pout·3Bout 6   0.75   0.98   1.00 yes 4a1c 01 2Pout·3Bout 6   0.75   0.99   1.00 yes 3i1s A2 2Pout·3Bout 6   0.75   1.00   1.00 yes 3i1s A4 2Pout·3Bout 6   0.75   1.00   1.00 yes 3i21 A4 2Pout·3Bout 6   0.75   0.99   1.00 yes 2xzm 034 2Pout·3Bout 6   0.12   0.99   1.00 no 2i2p X57 2Pout·3Bout 6   0.97   1.00   1.00 yes 2xzm 060 2Pout·3Bout 6   0.13   1.00   1.00 no 4a1e 063 2Pout·3Bout 6   0.76   0.99   1.00 yes 4a1c 063 2Pout·3Bout 6   0.76   1.00   1.00 yes 2xzn 076 2Pout·3Bout 6   0.11   0.99   1.00 no 3q3z A83 2Pout·3Bout 6   0.75   1.00   0.89 yes 354d A203 2Pout·3Bout 6   0.80   0.78   0.70 yes 1yls B245 2Pout·3Bout 6   0.81   0.97   0.99 yes 4a1c 0325 2Pout·3Bout 6   0.75   0.99   1.00 yes 1yls D342 2Pout·3Bout 6   0.81   1.00   0.99 yes 1mms D397 2Pout·3Bout 5   0.42   0.65   0.81 no 1nuv B412 2Pout·3Bout 6   0.70   0.80   0.93 yes 1nuv H415 2Pout·3Bout 6   0.80   0.89   0.84 yes 1nuj B419 2Pout·3Bout 6   0.72   0.88   0.82 yes 1nuj H422 2Pout·3Bout 6   0.70   0.89   0.93 yes 1n78 C700 2Pout·3Bout 6   0.91   0.86   0.91 yes 1n78 D701 2Pout·3Bout 6   0.80   0.90   0.96 yes 3ora A1535 2Pout·3Bout 6   0.75   0.99   0.94 yes 3ofx A1535 2Pout·3Bout 6   0.75   0.99   0.47 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>