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 6 of 67 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3d5b A3258 2Ob 2   0.03   0.22   0.14 no 4dr2 A1914 2Ob 2   0.03   0.18   0.86 no 3mrz A2940 2Ob 2   0.03   0.15   0.79 no 4lf7 A1788 2Ob 2   0.03   0.17   0.88 no 4lf8 A1788 2Ob 2   0.03   0.17   0.88 no 4dr3 A1762 2Ob 2   0.03   0.16   0.81 no 4qcp A3085 2Ob 2   0.03   0.18   0.94 no 2uxc Z80 2Ob 2   0.03   0.17   0.76 no 4dhb A1695 2Ob 2   0.03   0.16   0.74 no 4dv6 A1685 2Ob 2   0.03   0.14   0.95 no 4dr4 A1862 2Ob 2   0.03   0.20   0.40 no 4dr2 A1813 2Ob 2   0.03   0.15   0.85 no 4ji8 A1742 2Ob 2   0.03   0.15   0.88 no 4qcx B3007 2Ob 2   0.03   0.25   0.97 no 3kis a1653 2Ob 2   0.03   0.16   0.92 no 3huz A3097 2Ob 2   0.03   0.20   0.89 no 3d5b A3532 2Ob 2   0.03   0.16   0.30 no 4qcy X3007 2Ob 2   0.03   0.62   0.70 no 4nvu A3022 2Ob 2   0.03   0.19   0.87 no 3v27 A3183 2Ob 2   0.03   0.16   0.64 no 4dr1 A1643 2Ob 2   0.03   0.17   0.79 no 1un6 F309 2Ob 2   0.03   0.15   0.96 no 4lfb A1722 2Ob 2   0.03   0.15   0.93 no 4dv2 A1759 2Ob 2   0.03   0.22   0.80 no 3f1f A5597 2Ob 2   0.03   0.18   0.82 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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