MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbd:A2237, See in JSmolClick on the image to toggle views Site type: Oph·Ob Schematic drawing for Oph·Ob List of all 2305 Mg2+ binding sites with the site type Oph·Ob 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 1 of 93 | « 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 1fjg A1586 Oph·Ob 2   0.02   0.27   0.37 no 1fjg A1584 Oph·Ob 2   0.27   0.18   0.63 no 1fjg A1580 Oph·Ob 2   0.34   0.80   0.77 no 1fjg A1590 Oph·Ob 2   0.21   0.18   0.66 no 1hc8 D1367 Oph·Ob 2   0.37   0.55   0.87 no 1hc8 C1167 Oph·Ob 2   0.35   0.82   0.76 no 1hnw A1550 Oph·Ob 2   0.05   0.13   0.46 no 1hnw A1578 Oph·Ob 2   0.42   0.73   0.54 no 1hnw A1588 Oph·Ob 2   0.31   0.26   0.64 no 1hnw A1582 Oph·Ob 2   0.28   0.60   0.48 no 1hnx A1583 Oph·Ob 2   0.44   0.31   0.54 no 1hnx A1589 Oph·Ob 2   0.25   0.33   0.62 no 1hnx A1579 Oph·Ob 2   0.42   0.92   0.53 no 1hnz A1583 Oph·Ob 2   0.36   0.49   0.62 no 1hnz A1589 Oph·Ob 2   0.19   0.27   0.74 no 1hnz A1579 Oph·Ob 2   0.53   0.64   0.58 no 1hr0 A1578 Oph·Ob 2   0.42   0.76   0.71 no 1hr0 A1588 Oph·Ob 2   0.34   0.35   0.66 no 1hr0 A1582 Oph·Ob 2   0.35   0.35   0.75 no 1hr0 A1584 Oph·Ob 2   0.03   0.29   0.35 no 1i94 A1530 Oph·Ob 2   0.20   0.62   0.83 no 1i94 A1532 Oph·Ob 2   0.06   0.41   0.84 no 1i94 A1569 Oph·Ob 2   0.10   0.40   0.97 no 1i95 A1533 Oph·Ob 2   0.04   0.73   0.84 no 1i95 A1531 Oph·Ob 2   0.07   0.58   0.81 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>