MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoz:B2982, See in JSmolClick on the image to toggle views Site type: Pout·3Bout Schematic drawing for Pout·3Bout List of all 472 Mg2+ binding sites with the site type Pout·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 19 | « 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 2nz4 P9005 Pout·3Bout 6   0.97   0.82   0.92 yes 2nz4 S9004 Pout·3Bout 6   0.74   0.90   0.97 yes 2nz4 R9002 Pout·3Bout 6   0.76   0.92   0.99 yes 1q7y A8111 Pout·3Bout 4   0.91   0.29   0.42 no 1vq6 08100 Pout·3Bout 3   0.23   0.48   0.88 no 1w2b 38071 Pout·3Bout 5   0.17   0.40   0.51 no 1yj9 08071 Pout·3Bout 5   0.65   0.70   0.54 yes 4bpn A5070 Pout·3Bout 6   0.75   0.99   1.00 yes 4bpp A5025 Pout·3Bout 6   0.74   0.99   1.00 yes 4bpe A5025 Pout·3Bout 6   0.74   0.99   1.00 yes 4bpp A5010 Pout·3Bout 6   0.75   1.00   1.00 yes 4bpo A5001 Pout·3Bout 6   0.75   1.00   1.00 yes 2vho Z4020 Pout·3Bout 3   0.13   0.47   0.35 no 2vhm Z4020 Pout·3Bout 5   0.16   0.61   0.45 no 4dha A3752 Pout·3Bout 4   0.48   0.94   0.80 no 4dha A3726 Pout·3Bout 6   0.68   0.96   0.58 yes 4dha A3707 Pout·3Bout 6   0.63   0.84   0.75 yes 3v2d A3692 Pout·3Bout 6   0.78   0.99   0.94 yes 3v2d A3675 Pout·3Bout 5   0.62   0.80   0.89 yes 4qct A3653 Pout·3Bout 4   0.50   0.99   0.89 no 3v27 A3650 Pout·3Bout 6   0.73   1.00   0.55 yes 3v27 A3647 Pout·3Bout 6   0.73   0.97   0.79 yes 4dha A3642 Pout·3Bout 6   0.79   0.96   0.84 yes 4dhc A3639 Pout·3Bout 5   0.62   0.82   0.97 yes 4qct A3639 Pout·3Bout 2   0.14   0.10   0.81 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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