MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2v48:G2217, See in JSmolClick on the image to toggle views Site type: Oph·Ob·Nb Schematic drawing for Oph·Ob·Nb List of all 149 Mg2+ binding sites with the site type Oph·Ob·Nb 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 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3v2c A1652 Oph·Ob·Nb 5   0.33   0.54   0.87 no 1vxt A3204 Oph·Ob·Nb 3   0.32   0.18   0.70 no 2j00 Z217 Oph·Ob·Nb 3   0.32   0.35   0.92 no 4qcr A3641 Oph·Ob·Nb 5   0.29   0.47   0.72 no 4btd A4133 Oph·Ob·Nb 3   0.27   0.14   0.80 no 4kj8 A1628 Oph·Ob·Nb 3   0.26   0.19   0.91 no 1vqm 08094 Oph·Ob·Nb 4   0.25   0.76   0.56 no 3v6u A1712 Oph·Ob·Nb 3   0.23   0.66   0.87 no 3kno A2965 Oph·Ob·Nb 3   0.23   0.18   0.34 no 3oi3 B189 Oph·Ob·Nb 3   0.23   0.32   0.86 no 3g4s 08020 Oph·Ob·Nb 6   0.23   0.56   0.83 no 1vq8 08094 Oph·Ob·Nb 4   0.22   0.62   0.53 no 3cxc 98095 Oph·Ob·Nb 4   0.21   0.48   0.87 no 4qd1 A3146 Oph·Ob·Nb 3   0.21   0.20   1.00 no 1vqn 08094 Oph·Ob·Nb 4   0.20   0.70   0.67 no 4e8r A415 Oph·Ob·Nb 4   0.20   0.30   0.86 no 2vhp Z4039 Oph·Ob·Nb 6   0.19   0.58   0.98 no 4kjc A1623 Oph·Ob·Nb 6   0.19   0.65   0.88 no 2vhn Z4037 Oph·Ob·Nb 6   0.19   0.87   0.79 no 3i8g A2105 Oph·Ob·Nb 3   0.19   0.23   0.80 no 4too A3145 Oph·Ob·Nb 3   0.19   0.29   0.73 no 1vqp 08094 Oph·Ob·Nb 4   0.18   0.58   0.62 no 2vho Z4050 Oph·Ob·Nb 5   0.18   0.71   0.57 no 4qcz A3583 Oph·Ob·Nb 4   0.18   0.49   0.71 no 1vql 08094 Oph·Ob·Nb 4   0.18   0.69   0.60 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>