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 16 of 67 | « Previous | Next » | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3v2d A3278 2Ob 4   0.25   0.38   0.92 no 4qcz A3275 2Ob 2   0.11   0.08   0.91 no 3pyr A3274 2Ob 2   0.03   0.19   0.97 no 3v2d A3274 2Ob 5   0.40   0.61   0.93 no 4qd1 A3267 2Ob 2   0.04   0.21   0.94 no 4qd1 A3265 2Ob 2   0.05   0.27   1.00 no 3kni A3264 2Ob 2   0.05   0.19   0.41 no 4qcx A3263 2Ob 2   0.06   0.23   0.66 no 4qcv A3262 2Ob 2   0.05   0.16   0.87 no 3v2d A3260 2Ob 4   0.28   0.44   0.98 no 4qcv A3258 2Ob 2   0.05   0.49   0.70 no 3d5b A3258 2Ob 2   0.03   0.22   0.14 no 3v2d A3258 2Ob 6   0.52   0.74   1.00 yes 4qct A3258 2Ob 3   0.16   0.22   0.81 no 4qcp A3255 2Ob 3   0.15   0.22   0.92 no 4qct A3249 2Ob 3   0.14   0.56   0.95 no 4qcr A3248 2Ob 2   0.04   0.18   0.85 no 4qd1 A3247 2Ob 3   0.09   0.41   0.93 no 3v29 A3243 2Ob 2   0.04   0.16   0.80 no 4nvx A3242 2Ob 5   0.40   0.51   1.00 no 1vvo A3239 2Ob 2   0.04   0.22   0.82 no 3v2d A3238 2Ob 5   0.38   0.73   0.96 no 3v23 A3237 2Ob 2   0.03   0.23   0.81 no 3sgf A3235 2Ob 2   0.04   0.21   0.99 no 1vxt A3235 2Ob 2   0.07   0.23   0.58 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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