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 3 of 67 | « 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 3mrz A2984 2Ob 2   0.03   0.22   0.99 no 2uxc Z102 2Ob 2   0.04   0.23   0.95 no 4lf9 A1708 2Ob 2   0.05   0.19   0.72 no 3ms1 A2993 2Ob 2   0.04   0.28   0.77 no 3v23 A3109 2Ob 2   0.04   0.18   0.69 no 4b3r A2654 2Ob 2   0.05   0.15   0.98 no 3ms1 A3005 2Ob 2   0.04   0.32   0.44 no 3kit A3007 2Ob 2   0.04   0.15   0.85 no 3kiy A3006 2Ob 2   0.04   0.17   0.61 no 3knl A1640 2Ob 2   0.09   0.19   0.67 no 3ohz A3018 2Ob 2   0.03   0.22   0.82 no 4b3t A2657 2Ob 2   0.04   0.21   0.91 no 4dr3 A1717 2Ob 3   0.20   0.17   0.89 no 3kiu a1657 2Ob 2   0.03   0.19   0.95 no 3ohk A3027 2Ob 2   0.06   0.17   0.86 no 3pyt A2986 2Ob 2   0.06   0.19   0.70 no 4dv0 A1730 2Ob 2   0.03   0.17   0.66 no 3oi3 A3030 2Ob 2   0.06   0.12   0.92 no 3t1h A1737 2Ob 2   0.06   0.50   0.40 no 4kx2 A3132 2Ob 2   0.04   0.12   0.29 no 4ji0 A1736 2Ob 2   0.06   0.14   0.84 no 4dv7 A1739 2Ob 2   0.03   0.16   0.92 no 3v2f A3134 2Ob 3   0.06   0.40   0.81 no 4duy A1737 2Ob 2   0.04   0.85   0.73 no 3ivn A101 2Ob 2   0.03   0.17   0.91 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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