MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2v:B2959, See in JSmolClick on the image to toggle views Site type: Pout·Rout·3Bout Schematic drawing for Pout·Rout·3Bout List of all 45 Mg2+ binding sites with the site type Pout·Rout·3Bout 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1fuf A97 Pout·Rout·3Bout 5   0.85   0.86   0.88 yes 1qvg 08076 Pout·Rout·3Bout 6   0.40   0.82   0.64 no 1vql 08108 Pout·Rout·3Bout 5   0.22   0.82   0.70 no 1vqp 08108 Pout·Rout·3Bout 5   0.35   0.86   0.66 no 1vs5 A1599 Pout·Rout·3Bout 6   0.98   0.99   1.00 yes 2i2v B2959 Pout·Rout·3Bout 6   0.97   1.00   1.00 yes 2qow A1546 Pout·Rout·3Bout 6   0.97   1.00   1.00 yes 2qp1 B2957 Pout·Rout·3Bout 6   0.97   0.99   1.00 yes 2xzm 015 Pout·Rout·3Bout 6   0.12   0.99   1.00 no 2xzn 041 Pout·Rout·3Bout 6   0.11   0.99   1.00 no 2z4l B2983 Pout·Rout·3Bout 6   0.97   1.00   1.00 yes 3df1 A2219 Pout·Rout·3Bout 6   0.97   1.00   1.00 yes 3i1r A2941 Pout·Rout·3Bout 6   0.76   0.99   1.00 yes 3oat A2940 Pout·Rout·3Bout 6   0.76   0.98   0.55 yes 3oat A2982 Pout·Rout·3Bout 6   0.76   0.98   0.55 yes 3ofr A2984 Pout·Rout·3Bout 6   0.76   0.98   0.59 yes 3ofz A2982 Pout·Rout·3Bout 6   0.75   1.00   0.69 yes 3v27 A3597 Pout·Rout·3Bout 4   0.54   0.94   0.82 yes 3v27 A3573 Pout·Rout·3Bout 4   0.51   0.93   0.97 yes 3v29 A3550 Pout·Rout·3Bout 4   0.47   0.66   0.66 no 3v2d A3455 Pout·Rout·3Bout 3   0.37   0.64   0.66 no 4bpe A5001 Pout·Rout·3Bout 6   0.75   1.00   1.00 yes 4bpn A5025 Pout·Rout·3Bout 6   0.75   0.99   1.00 yes 4bpn A5001 Pout·Rout·3Bout 6   0.74   1.00   1.00 yes 4bpo A5025 Pout·Rout·3Bout 6   0.75   0.99   1.00 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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