MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·2Bout Schematic drawing for 2Pout·2Bout List of all 453 Mg2+ binding sites with the site type 2Pout·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 12 of 19 | « Previous | Next » | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4bpn A5062 2Pout·2Bout 6   0.74   1.00   1.00 yes 4tom A3092 2Pout·2Bout 6   0.74   0.98   0.76 yes 2qam B3521 2Pout·2Bout 6   0.97   0.99   1.00 yes 2qbe B3521 2Pout·2Bout 6   0.97   1.00   0.50 yes 3i1r A2996 2Pout·2Bout 6   0.75   0.99   1.00 yes 3i1n A2996 2Pout·2Bout 6   0.75   0.99   0.55 yes 4ji1 A1781 2Pout·2Bout 6   0.96   1.00   0.90 yes 4dr5 A1834 2Pout·2Bout 6   0.95   1.00   0.64 yes 3or9 A1535 2Pout·2Bout 6   0.74   0.99   0.48 no 3ofo A1535 2Pout·2Bout 6   0.75   0.99   0.32 no 2xzn 088 2Pout·2Bout 6   0.13   0.99   1.00 no 2xzm 088 2Pout·2Bout 6   0.14   0.99   1.00 no 3ofc A3017 2Pout·2Bout 6   0.74   0.98   0.47 no 4tpd A3116 2Pout·2Bout 6   0.74   0.99   0.45 no 3i1n A3019 2Pout·2Bout 6   0.75   0.99   0.48 no 4tom A3119 2Pout·2Bout 6   0.72   0.99   0.18 no 3oat A3036 2Pout·2Bout 6   0.75   0.98   0.43 no 4dr5 A1823 2Pout·2Bout 6   0.96   1.00   0.42 no 4dr7 A1835 2Pout·2Bout 6   0.94   0.97   0.39 no 4ji8 A1921 2Pout·2Bout 6   0.92   0.98   0.38 no 4ji8 A1970 2Pout·2Bout 6   0.95   0.99   0.38 no 3v29 A3418 2Pout·2Bout 6   0.71   0.98   0.47 no 4tol A1601 2Pout·2Bout 6   0.74   0.99   0.76 yes 3oaq A1 2Pout·2Bout 6   0.75   0.99   0.97 yes 4pe9 A1602 2Pout·2Bout 6   0.74   0.98   0.85 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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