MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3i20:A2925, See in JSmolClick on the image to toggle views Site type: Ob Schematic drawing for Ob List of all 4324 Mg2+ binding sites with the site type 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 173 | « 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 1dfu M501 Ob 6   0.94   0.77   0.74 yes 1f27 A35 Ob 4   0.59   0.64   0.78 yes 1feu E315 Ob 5   0.50   0.41   0.65 no 1ffy T1204 Ob 6   0.62   0.82   0.99 yes 1fjg A1551 Ob 1   0.02  0   0.48 no 1fjg A1615 Ob 1   0.01  0   0.45 no 1fjg A1572 Ob 1   0.07  0   0.42 no 1fjg A210 Ob 1   0.04  0   0.61 no 1gid A265 Ob 1   0.18  0   0.70 no 1gid B266 Ob 1   0.16  0   0.67 no 1hnw A211 Ob 1   0.01  0   0.86 no 1hnw A1607 Ob 1   0.02  0   0.33 no 1hnw A1566 Ob 1   0.03  0   0.81 no 1hnw A1584 Ob 1   0.03  0   0.32 no 1hnw A210 Ob 1   0.01  0   0.58 no 1hnw A1571 Ob 1   0.05  0   0.31 no 1hnx A1585 Ob 1   0.03  0   0.55 no 1hnx A210 Ob 1   0.03  0   0.64 no 1hnx A1571 Ob 1   0.06  0   0.40 no 1hnx A1545 Ob 1   0.02  0   0.63 no 1hnx A1549 Ob 1   0.03  0   0.84 no 1hnz A210 Ob 1   0.02  0   0.59 no 1hnz A1549 Ob 1   0.01  0   0.79 no 1hnz A1571 Ob 1   0.06  0   0.42 no 1hnz A1550 Ob 1   0.01  0   0.47 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].

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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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