MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 2wdm 2WDM (3.5Å) -- RIBOSOME : Structure of the thermus thermophilus 70s ribosome in complex with mrna, paromomycin, acylated a- and p-site trnas, and e-site trna. this file contains the 30s subunit a-,p-, and e-site trnas and paromomycin for molecule ii. List of all 273 Mg2+ binding sites in the PDB structure 2wdm 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 #", "Site type" or "Mg2+ ID" Page 1 of 14 | « 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 2wdm Z200 Or 1   0.01  0   0.66 no 2wdm Z736 Or 2   0.15   0.39   0.94 no 2wdm Z510 Or 1   0.05  0   0.74 no 2wdm Z518 Or 1   0.04  0   0.85 no 2wdm Z527 Or 2   0.22   0.14   0.42 no 2wdm Z179 Ob 1   0.02  0   0.58 no 2wdm Z161 Ob 1   0.07  0   0.54 no 2wdm Z210 Ob 1   0.01  0   0.78 no 2wdm Z45 Ob 1   0.09  0   0.88 no 2wdm Z499 Ob 1   0.01  0   0.54 no 2wdm Z4 Ob 1   0.05  0   0.89 no 2wdm Z213 Ob 1   0.21  0   0.68 no 2wdm Z207 Ob 1   0.01  0   0.66 no 2wdm Z176 Ob 1   0.01  0   0.85 no 2wdm Z521 Ob 1   0.03  0   0.77 no 2wdm Z152 Ob 2   0.15   0.16   0.61 no 2wdm Z534 Ob 1   0.02  0   0.66 no 2wdm Z42 Ob 1   0.13  0   0.47 no 2wdm Z215 Ob 1   0.03  0   0.83 no 2wdm Z283 Ob 1   0.01  0   0.96 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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