MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qam:B3090, See in JSmolClick on the image to toggle views Site type: Oph·2Pout Schematic drawing for Oph·2Pout List of all 2450 Mg2+ binding sites with the site type Oph·2Pout 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 98 | « 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 4dr4 A1635 Oph·2Pout 2   0.16   0.04   0.98 no 4nw1 A3529 Oph·2Pout 2   0.14   0.04   0.95 no 2vhp Z4049 Oph·2Pout 2   0.08   0.05   0.91 no 4nxn A1652 Oph·2Pout 2   0.18   0.05   0.44 no 4kj9 A3024 Oph·2Pout 3   0.63   0.05   0.50 no 4qd1 A3316 Oph·2Pout 2   0.15   0.06   1.00 no 4kj9 A3025 Oph·2Pout 2   0.45   0.08   0.21 no 1q7y A8049 Oph·2Pout 2   0.51   0.08   1.00 no 4nvz A3545 Oph·2Pout 2   0.16   0.09   0.63 no 4qcy A3207 Oph·2Pout 2   0.14   0.09   0.93 no 4nw0 A3097 Oph·2Pout 2   0.14   0.09   0.87 no 4nw1 A3238 Oph·2Pout 2   0.16   0.10   0.92 no 4kiy A1625 Oph·2Pout 3   0.22   0.11   0.43 no 4nvz A3548 Oph·2Pout 2   0.16   0.11   0.46 no 1q81 A8049 Oph·2Pout 2   0.39   0.11   0.94 no 4kjb A3058 Oph·2Pout 3   0.43   0.12   0.61 no 4dr6 A1616 Oph·2Pout 2   0.17   0.12   0.47 no 3cxc 08049 Oph·2Pout 2   0.15   0.12   0.99 no 4nw1 A3623 Oph·2Pout 2   0.14   0.13   0.54 no 4kja A1605 Oph·2Pout 3   0.33   0.13   0.70 no 4qcr A3063 Oph·2Pout 2   0.08   0.13   0.93 no 4kiz A3117 Oph·2Pout 3   0.45   0.14   0.95 no 1vqn 08072 Oph·2Pout 2   0.09   0.14   0.69 no 3v23 A3294 Oph·2Pout 2   0.16   0.15   0.90 no 4dr7 A1617 Oph·2Pout 2   0.16   0.15   0.58 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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