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 2xzn 016 Pout·3Bout 6   0.12   1.00   1.00 no 2xzn 026 Pout·3Bout 6   0.12   1.00   1.00 no 4qcs A3087 Pout·3Bout 1   0.12  0   0.95 no 2xzn 025 Pout·3Bout 6   0.12   1.00   1.00 no 2vho Z4020 Pout·3Bout 3   0.13   0.47   0.35 no 2xzm 026 Pout·3Bout 6   0.13   1.00   1.00 no 4qct A3639 Pout·3Bout 2   0.14   0.10   0.81 no 2vhm Z4020 Pout·3Bout 5   0.16   0.61   0.45 no 1w2b 38071 Pout·3Bout 5   0.17   0.40   0.51 no 1vq6 08100 Pout·3Bout 3   0.23   0.48   0.88 no 4qd1 A3457 Pout·3Bout 2   0.25   0.28   0.64 no 4qcu A3169 Pout·3Bout 2   0.25   0.28   0.87 no 4qcq A3215 Pout·3Bout 2   0.25   0.28   0.89 no 4nvz A3561 Pout·3Bout 2   0.25   0.26   0.80 no 4qcr A3394 Pout·3Bout 2   0.25   0.28   0.90 no 4nvv A3565 Pout·3Bout 2   0.25   0.27   0.78 no 4dhc A3401 Pout·3Bout 2   0.26   0.35   0.69 no 4nvz A3394 Pout·3Bout 3   0.27   0.30   0.98 no 4kj5 A3129 Pout·3Bout 4   0.30   0.40   0.37 no 4ji0 A1622 Pout·3Bout 2   0.32   0.29   0.85 no 4kj7 A3060 Pout·3Bout 4   0.34   0.37   0.42 no 1mms C437 Pout·3Bout 5   0.35   0.77   0.91 no 3v2f A3320 Pout·3Bout 3   0.36   0.65   0.82 no 4nw1 A3301 Pout·3Bout 3   0.37   0.39   0.81 no 4dhb A1794 Pout·3Bout 3   0.37   0.66   0.98 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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