MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·2Bout Schematic drawing for 2Pout·2Bout List of all 453 Mg2+ binding sites with the site type 2Pout·2Bout 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 19 | « 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 1mms C273 2Pout·2Bout 5   0.33   0.46   0.91 no 4gau E301 2Pout·2Bout 6   0.75   1.00   0.92 yes 3cul C503 2Pout·2Bout 2   0.48   0.70   0.89 no 3p49 A738 2Pout·2Bout 4   0.50   0.98   0.99 yes 3i1z A1535 2Pout·2Bout 6   0.74   0.99   1.00 yes 3ofo A1535 2Pout·2Bout 6   0.75   0.99   0.32 no 3or9 A1535 2Pout·2Bout 6   0.74   0.99   0.48 no 3i1m A1535 2Pout·2Bout 6   0.75   0.99   0.35 no 3ofp A1535 2Pout·2Bout 6   0.75   0.99   0.95 yes 3ofa A1535 2Pout·2Bout 6   0.75   1.00   0.46 no 3i1q A1537 2Pout·2Bout 6   0.75   1.00   1.00 yes 3oaq A1537 2Pout·2Bout 6   0.75   1.00   0.73 yes 3i1s A1541 2Pout·2Bout 6   0.75   1.00   1.00 yes 3i21 A1541 2Pout·2Bout 6   0.75   1.00   1.00 yes 3i1o A1541 2Pout·2Bout 6   0.75   1.00   0.68 yes 3i1z A1544 2Pout·2Bout 6   0.75   1.00   1.00 yes 3ofo A1544 2Pout·2Bout 6   0.75   0.98   0.94 yes 3i1q A1544 2Pout·2Bout 6   0.75   1.00   1.00 yes 2qoy A1545 2Pout·2Bout 6   0.97   0.99   1.00 yes 2qbj A1546 2Pout·2Bout 6   0.97   1.00   1.00 yes 3oar A1549 2Pout·2Bout 6   0.75   1.00   0.96 yes 2i2p A1550 2Pout·2Bout 6   0.97   1.00   1.00 yes 3i21 A1552 2Pout·2Bout 6   0.75   1.00   1.00 yes 2qbf A1563 2Pout·2Bout 6   0.97   0.99   1.00 yes 2z4m A1564 2Pout·2Bout 6   0.97   0.99   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>