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 19 of 67 | « Previous | Next » | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4qcr A3046 2Ob 2   0.14   0.09   0.87 no 3kiu a1580 2Ob 2   0.14   0.16   0.85 no 3pyo A2937 2Ob 2   0.07   0.22   0.48 no 3v2d A3046 2Ob 3   0.05   0.49   0.90 no 3ow2 08047 2Ob 2   0.05   0.18   0.61 no 4qcn A3047 2Ob 2   0.08   0.14   0.97 no 3uz6 A1871 2Ob 2   0.05   0.33   0.87 no 1vxi A1650 2Ob 2   0.03   0.19   0.89 no 4ox9 A1655 2Ob 2   0.07   0.20   0.89 no 4qco A3053 2Ob 2   0.11   0.09   0.91 no 4ji4 A1651 2Ob 3   0.21   0.31   0.75 no 4nxn A1650 2Ob 2   0.03   0.14   0.61 no 4l6j A4110 2Ob 2   0.06   0.18   0.67 no 3uzg A2008 2Ob 2   0.05   0.20   0.84 no 3uz3 A1864 2Ob 2   0.05   0.25   0.82 no 1vvz A1649 2Ob 2   0.42   0.06  0 no 1xnq A210 2Ob 2   0.05   0.18   0.91 no 4qcp A3050 2Ob 2   0.06   0.15   0.75 no 3knh A1575 2Ob 2   0.06   0.15   0.62 no 3uyd A1864 2Ob 2   0.04   0.35   0.81 no 1n32 A1598 2Ob 2   0.19   0.06   0.32 no 4ji2 A1652 2Ob 3   0.21   0.28   0.82 no 4qcz A3051 2Ob 3   0.12   0.32   0.77 no 3i8g A1586 2Ob 2   0.03   0.19   0.66 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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