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 11 of 67 | « Previous | Next » | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3oh5 A3179 2Ob 2   0.03   0.16   0.72 no 3oi5 A3054 2Ob 2   0.03   0.17   0.82 no 1vxn A3231 2Ob 2   0.03   0.20   0.47 no 4kfk A2301 2Ob 2   0.03   0.16   0.88 no 3pyo A2947 2Ob 2   0.03   0.14   0.81 no 4ji7 A2016 2Ob 2   0.03   0.20   0.74 no 3mrz A2984 2Ob 2   0.03   0.22   0.99 no 3t1y A1632 2Ob 2   0.03   0.16   0.31 no 3d5b A3497 2Ob 2   0.03   0.20   0.12 no 2j02 Z187 2Ob 2   0.03   0.20   0.86 no 3tvf A2611 2Ob 2   0.03   0.22   0.99 no 3uz6 A2285 2Ob 2   0.03   0.20   0.84 no 3v2d B205 2Ob 2   0.03   0.19   0.80 no 3ohk A3131 2Ob 2   0.03   0.13   0.76 no 3u5d 4330 2Ob 2   0.03   0.18   0.99 no 4l6j A4725 2Ob 2   0.03   0.17   0.54 no 4dh9 A1811 2Ob 2   0.03   0.20   0.58 no 1xmo A210 2Ob 2   0.03   0.15   0.36 no 4dv4 A1821 2Ob 2   0.03   0.65   0.53 no 4ji0 A1696 2Ob 2   0.03   0.18   0.73 no 4dr6 A1934 2Ob 2   0.03   0.18   0.97 no 4ji0 A1642 2Ob 2   0.03   0.17   0.85 no 2uxc Z3 2Ob 2   0.03   0.26   0.98 no 4dv4 A1742 2Ob 2   0.03   0.18   0.85 no 4lf9 A1608 2Ob 2   0.03   0.18   0.85 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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