MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qow:A1583, See in JSmolClick on the image to toggle views Site type: Or Schematic drawing for Or List of all 1520 Mg2+ binding sites with the site type Or 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 61 | « 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 1duh A2 Or 1   0.25  0   0.77 no 1evv A908 Or 3   0.36   0.21   0.44 no 1feu C318 Or 1   0.34  0   0.96 no 1feu F323 Or 2   0.25   0.15   0.94 no 1fjg A1571 Or 1   0.02  0   0.59 no 1fjg A1619 Or 1   0.02  0   0.46 no 1hnx A1621 Or 1   0.18  0   0.09 no 1hr0 W72 Or 2   0.17   0.18   0.49 no 1i94 A1572 Or 1   0.02  0   0.71 no 1i94 A1522 Or 1   0.05  0   0.55 no 1i94 A1553 Or 1   0.01  0   0.66 no 1i94 A1538 Or 2   0.26   0.17   0.62 no 1i95 A1540 Or 1   0.05  0   0.70 no 1i95 A1575 Or 1   0.03  0   0.68 no 1i96 A1540 Or 1   0.08  0   0.76 no 1i96 A1555 Or 1   0.02  0   0.69 no 1i96 A1574 Or 1   0.03  0   0.72 no 1i97 A1523 Or 1   0.02  0   0.69 no 1i97 A1574 Or 1   0.02  0   0.88 no 1i97 A1540 Or 1   0.14  0   0.60 no 1ibk A1630 Or 1   0.02  0   0.48 no 1ibl A1571 Or 2   0.30   0.19   0.20 no 1ibm A1610 Or 1   0.02  0   0.62 no 1ibm A1642 Or 1   0.01  0   0.45 no 1ibm A1634 Or 1   0.03  0   0.55 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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