MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2r8s:R1004, See in JSmolClick on the image to toggle views Site type: 2Ob Schematic drawing for 2Ob List of all 1662 Mg2+ binding sites with the site type 2Ob 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 67 | « 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 4dv2 A1664 2Ob 2   0.03   0.25   0.97 no 4nvz B3006 2Ob 2   0.03   0.15   0.84 no 1ibk A1614 2Ob 2   0.03   0.13   0.46 no 3sgf A3153 2Ob 2   0.03   0.53   0.98 no 4nvu A3030 2Ob 2   0.03   0.12   0.87 no 3mrz A2954 2Ob 2   0.03   0.19   0.47 no 4tp2 A1655 2Ob 2   0.03   0.21   0.90 no 4dr3 A1766 2Ob 2   0.03   0.66   0.95 no 4nvz A3056 2Ob 2   0.03   0.17   0.79 no 4dv7 A1791 2Ob 2   0.03   0.14   0.84 no 3pyo A2989 2Ob 2   0.03   0.11   0.52 no 3ohz A166 2Ob 2   0.03   0.20   0.80 no 4ji4 A1710 2Ob 2   0.03   0.19   0.80 no 4dv5 A1748 2Ob 2   0.03   0.29   0.70 no 4eja A7134 2Ob 2   0.03   0.12   0.39 no 4lf6 A1723 2Ob 2   0.03   0.15   0.72 no 3ohk A3122 2Ob 2   0.03   0.19   0.77 no 1hr0 A1547 2Ob 2   0.03   0.14   0.81 no 3pyr A3028 2Ob 2   0.03   0.17   0.60 no 2j02 Z202 2Ob 2   0.03   0.16   0.37 no 3v2d A3075 2Ob 2   0.03   0.46   0.95 no 4qd1 A3037 2Ob 2   0.03   0.20   1.00 no 1ibk A1548 2Ob 2   0.03   0.20   0.58 no 3uz6 A2261 2Ob 2   0.03   0.15   0.84 no 3kno A2998 2Ob 2   0.03   0.16   0.22 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>