MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4k:A1600, See in JSmolClick on the image to toggle views Site type: Rout·2Bout Schematic drawing for Rout·2Bout List of all 85 Mg2+ binding sites with the site type Rout·2Bout 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 1 of 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1k8a A8076 Rout·2Bout 4   0.52   0.68   0.68 yes 1k9m A8076 Rout·2Bout 5   0.59   0.67   0.86 yes 1kd1 A8076 Rout·2Bout 5   0.49   0.71   0.90 no 1q7y A8076 Rout·2Bout 4   0.40   0.54   0.53 no 1vq5 28076 Rout·2Bout 5   0.33   0.63   0.75 no 1vqk 08076 Rout·2Bout 4   0.21   0.50   0.68 no 1vql 08076 Rout·2Bout 4   0.21   0.71   0.67 no 1vqm 28076 Rout·2Bout 5   0.20   0.75   0.73 no 1yi2 28076 Rout·2Bout 4   0.24   0.47   0.95 no 1yij 28076 Rout·2Bout 4   0.27   0.42   0.69 no 1yj9 28076 Rout·2Bout 4   0.32   0.36   0.59 no 1yjw 78076 Rout·2Bout 3   0.41   0.50   0.86 no 2fqn A202 Rout·2Bout 6   0.97   0.96   0.98 yes 2xzm 068 Rout·2Bout 6   0.13   1.00   1.00 no 2xzn 060 Rout·2Bout 6   0.11   1.00   1.00 no 2xzn 036 Rout·2Bout 6   0.12   0.99   1.00 no 2z4k A1600 Rout·2Bout 6   0.97   1.00   1.00 yes 3cce 08060 Rout·2Bout 5   0.28   0.81   0.88 no 3ccm 08060 Rout·2Bout 5   0.13   0.46   0.77 no 3ccq 08060 Rout·2Bout 5   0.18   0.54   0.87 no 3ccr 28060 Rout·2Bout 4   0.12   0.53   0.91 no 3ccs 08060 Rout·2Bout 4   0.21   0.66   0.72 no 3ccu 08060 Rout·2Bout 4   0.25   0.61   0.96 no 3cma 08085 Rout·2Bout 2   0.04   0.15   0.76 no 3cma 28060 Rout·2Bout 3   0.09   0.35   0.96 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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