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 20 of 67 | « Previous | Next » | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2v48 G2221 2Ob 2   0.12   0.20   0.24 no 4byd A2543 2Ob 2   0.12   0.40   0.60 no 3g4s 08032 2Ob 4   0.12   0.69   0.96 no 4b3m A2749 2Ob 2   0.12   0.17   0.87 no 3r1l C1036 2Ob 2   0.12   0.08   0.97 no 4nxn A1780 2Ob 3   0.12   0.72   0.79 no 1vvu A3149 2Ob 2   0.12   0.25   0.29 no 1vxl A3117 2Ob 2   0.12   0.14   0.20 no 2wdh Z65 2Ob 2   0.12   0.05   0.92 no 4ji2 A1825 2Ob 2   0.11   0.16   0.89 no 4kjb A3055 2Ob 4   0.11   0.53   0.95 no 4b3r A2558 2Ob 2   0.11   0.43   0.79 no 3ccr 08032 2Ob 5   0.11   0.56   0.84 no 3cme 08076 2Ob 5   0.11   0.50   0.65 no 2j00 Z161 2Ob 2   0.11   0.28   0.24 no 4b3t A2641 2Ob 2   0.11   0.27   0.85 no 4qco A3053 2Ob 2   0.11   0.09   0.91 no 3kis a1622 2Ob 2   0.11   0.18   0.60 no 2v46 Z161 2Ob 2   0.11   0.25   0.55 no 1vy3 A3167 2Ob 2   0.11   0.24   0.29 no 4qcz A3275 2Ob 2   0.11   0.08   0.91 no 2pn3 A2 2Ob 2   0.11   0.10   0.61 no 2uxb G3108 2Ob 2   0.11   0.08   0.58 no 4byd A2594 2Ob 2   0.11   0.20   0.93 no 1vxl A3171 2Ob 2   0.11   0.25   0.76 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>