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 10 of 12 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3ofr A2921 2Pout·3Bout 6   0.76   0.98   0.83 yes 3oat A2920 2Pout·3Bout 6   0.75   0.98   0.70 yes 4ji7 A1850 2Pout·3Bout 6   0.96   0.99   0.72 yes 4tp9 A3019 2Pout·3Bout 6   0.76   0.99   0.48 no 1vq5 08071 2Pout·3Bout 6   0.43   0.77   0.89 no 1qvg 08071 2Pout·3Bout 6   0.93   0.86   0.49 no 1n8r A8071 2Pout·3Bout 6   0.74   0.88   0.40 no 2xzn 076 2Pout·3Bout 6   0.11   0.99   1.00 no 4tpd A3085 2Pout·3Bout 6   0.74   0.98   0.43 no 4ji5 A1716 2Pout·3Bout 6   0.95   0.98   0.30 no 3ofd A3031 2Pout·3Bout 6   0.74   0.99   0.30 no 3ofd A3033 2Pout·3Bout 6   0.73   0.98   0.34 no 4ji6 A1763 2Pout·3Bout 6   0.93   0.99   0.42 no 4dv1 A1801 2Pout·3Bout 6   0.92   0.99   0.37 no 4dr7 A1869 2Pout·3Bout 6   0.94   0.97   0.37 no 4a1e 01 2Pout·3Bout 6   0.75   0.98   1.00 yes 1n78 C700 2Pout·3Bout 6   0.91   0.86   0.91 yes 3i1s A2 2Pout·3Bout 6   0.75   1.00   1.00 yes 3i1q A1535 2Pout·3Bout 6   0.75   0.99   1.00 yes 1n78 D701 2Pout·3Bout 6   0.80   0.90   0.96 yes 2qb9 A2014 2Pout·3Bout 6   0.97   1.00   1.00 yes 1nuj B419 2Pout·3Bout 6   0.72   0.88   0.82 yes 3oar A1537 2Pout·3Bout 6   0.75   1.00   0.66 yes 3df3 A2016 2Pout·3Bout 6   0.97   1.00   1.00 yes 3i1s A4 2Pout·3Bout 6   0.75   1.00   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>