MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4m:A1592, See in JSmolClick on the image to toggle views Site type: Pout Schematic drawing for Pout List of all 731 Mg2+ binding sites with the site type Pout 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 30 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1jj2 A8105 Pout 2   0.03   0.20   0.66 no 1k73 C8105 Pout 2   0.03   0.19   0.13 no 1kc8 18105 Pout 2   0.03   0.18   0.73 no 1kqs Y8105 Pout 1   0.01  0   0.86 no 1m1k 18105 Pout 2   0.07   0.08   0.55 no 1m90 18105 Pout 1   0.01  0   0.61 no 1nji 18105 Pout 1   0.01  0   0.59 no 1q7y C8065 Pout 6   0.98   0.67   0.33 no 1q81 A8024 Pout 1   0.03  0   0.71 no 1q82 D8055 Pout 5   0.43   0.53   0.67 no 1q86 18105 Pout 1   0.03  0   0.67 no 1qvf Y8105 Pout 2   0.03   0.20   0.53 no 1qvf 08119 Pout 2   0.15   0.13   1.00 no 1qvg A8105 Pout 2   0.04   0.19   0.50 no 1vq8 08024 Pout 2   0.05   0.17   0.73 no 1vq9 A8066 Pout 3   0.45   0.43   0.99 no 1vqk A8066 Pout 3   0.30   0.53   0.98 no 1vqn A8066 Pout 2   0.44   0.11   0.94 no 1vqp A8066 Pout 2   0.47   0.11   0.97 no 1vt2 A2934 Pout 6   0.75   1.00   0.65 yes 1vt2 A2995 Pout 5   0.81   0.80   0.75 yes 1vt2 A3012 Pout 2   0.33   0.30   0.67 no 1vt2 E202 Pout 6   0.74   0.99   0.45 no 1vt2 A2919 Pout 6   0.74   1.00   0.69 yes 1vt2 A2907 Pout 6   0.74   1.00   0.75 yes

^# 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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