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 15 of 67 | « Previous | Next » | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dhc A3025 2Ob 2   0.04   0.14   0.82 no 4gkj A1626 2Ob 2   0.03   0.20   0.89 no 4g5v A1651 2Ob 2   0.08   0.20   0.92 no 4dv5 A1626 2Ob 4   0.33   0.35   0.76 no 3mrz A2917 2Ob 2   0.04   0.18   0.85 no 4dv7 A1627 2Ob 4   0.34   0.35   0.98 no 4qco A3029 2Ob 2   0.15   0.30   0.97 no 3v29 A3027 2Ob 3   0.05   0.32   0.92 no 2vqf Z29 2Ob 2   0.10   0.47   0.92 no 1vvl A1628 2Ob 2   0.05   0.13   0.69 no 1vvv A1628 2Ob 2   0.16   0.05   0.42 no 4nvx A3028 2Ob 2   0.05   0.20   0.89 no 1vvz A1628 2Ob 2   0.09   0.16   0.83 no 4ji0 A1630 2Ob 3   0.19   0.19   0.95 no 4nxn A1630 2Ob 4   0.35   0.40   0.56 no 4g5t A1672 2Ob 2   0.06   0.30   0.86 no 3i8g A1568 2Ob 2   0.14   0.27   0.94 no 4qcm A1631 2Ob 2   0.08   0.15   0.83 no 2uxb G3033 2Ob 2   0.04   0.22   0.54 no 4lfb A1640 2Ob 2   0.04   0.20   0.90 no 4nvx A3031 2Ob 2   0.03   0.17   0.76 no 4nvu A3030 2Ob 2   0.03   0.12   0.87 no 4qcp A3031 2Ob 2   0.09   0.10   0.64 no 4qcy A3031 2Ob 2   0.03   0.17   0.83 no 3v2d A3638 2Ob 5   0.27   0.64   0.89 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>