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 20 of 67 | « Previous | Next » | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4k27 U101 2Ob 2   0.16   0.28   0.68 no 2xg1 Z1742 2Ob 2   0.07   0.23   0.68 no 3oww A126 2Ob 3   0.10   0.36   0.68 no 1o3z A303 2Ob 4   0.09   0.61   0.68 no 1vvo A3187 2Ob 2   0.07   0.24   0.68 no 3knl A1615 2Ob 2   0.05   0.17   0.68 no 4nw1 A3165 2Ob 2   0.06   0.11   0.68 no 3f1e Y5510 2Ob 2   0.04   0.14   0.68 no 3ohc A1573 2Ob 2   0.03   0.18   0.68 no 2wdh Z234 2Ob 2   0.05   0.13   0.68 no 3f1e A5319 2Ob 2   0.06   0.15   0.68 no 4ji1 A1666 2Ob 2   0.05   0.61   0.68 no 3kni A3043 2Ob 2   0.04   0.19   0.69 no 3cma 08032 2Ob 6   0.16   0.91   0.69 no 2xfz Z1684 2Ob 2   0.08   0.16   0.69 no 1vvy A3198 2Ob 2   0.07   0.15   0.69 no 4nvz A3327 2Ob 3   0.17   0.24   0.69 no 1vvl A1628 2Ob 2   0.05   0.13   0.69 no 4nxm A1651 2Ob 3   0.19   0.25   0.69 no 4qcz A3109 2Ob 2   0.14   0.06   0.69 no 4fax A402 2Ob 2   0.07   0.14   0.69 no 4dv6 A1740 2Ob 2   0.04   0.14   0.69 no 3v23 A3109 2Ob 2   0.04   0.18   0.69 no 4lfa A1627 2Ob 2   0.04   0.13   0.69 no 4lf5 A1688 2Ob 2   0.05   0.20   0.69 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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