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 9 of 67 | « Previous | Next » | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4l6j A4998 2Ob 2   0.03   0.18   0.97 no 4l6j A4942 2Ob 2   0.04   0.16   0.75 no 4l6j A4869 2Ob 2   0.05   0.22   0.75 no 4l6j A4858 2Ob 2   0.04   0.23   0.57 no 4l6j A4856 2Ob 2   0.05   0.19   0.54 no 4l6j A4798 2Ob 2   0.04   0.14   0.60 no 4l6j A4725 2Ob 2   0.03   0.17   0.54 no 3u5d 14372 2Ob 2   0.03   0.15   0.95 no 3u5d 14210 2Ob 2   0.05   0.24   0.94 no 3u5d 14170 2Ob 2   0.03   0.22   0.74 no 4btd A4167 2Ob 2   0.13   0.06   0.92 no 4btd A4141 2Ob 2   0.03   0.17   0.81 no 3u5h 54136 2Ob 2   0.05   0.25   0.98 no 4btd A4130 2Ob 2   0.04   0.19   0.87 no 3u5h 54121 2Ob 2   0.03   0.37   0.73 no 3u5d 14116 2Ob 2   0.04   0.63   0.60 no 4l6j A4110 2Ob 2   0.06   0.18   0.67 no 4btd A4078 2Ob 2   0.06   0.21   0.89 no 3u5d 14060 2Ob 2   0.05   0.23   0.69 no 4btd A4058 2Ob 2   0.04   0.18   0.74 no 3u5d 14055 2Ob 2   0.05   0.19   0.97 no 4btd A4040 2Ob 2   0.08   0.24   0.47 no 4bye A4014 2Ob 2   0.27   0.06   0.62 no 3u5h 53998 2Ob 2   0.04   0.22   0.76 no 4bye A3994 2Ob 2   0.07   0.12   0.93 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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