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 2wdg 2WDG (3.3Å) -- RIBOSOME : Structure of the thermus thermophilus 70s ribosome in complex with mrna, paromomycin, acylated a-site trna, deacylated p-site trna, and e-site trna. this file contains the 30s subunit a-,p-, and e-site trnas and paromomycin for molecule i. List of all 319 Mg2+ binding sites in the PDB structure 2wdg 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 16 | « 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 2wdg Z488 Or 1   0.44  0   0.68 no 2wdg Z724 Or 1   0.08  0   0.23 no 2wdg Z727 Or 1   0.02  0   0.66 no 2wdg Z2 Or 1   0.18  0   0.94 no 2wdg Z187 Or 2   0.46   0.17   0.64 no 2wdg Z196 Or 1   0.02  0   0.58 no 2wdg Z222 Or 1   0.01  0   0.96 no 2wdg Z37 Or 2   0.22   0.15   0.77 no 2wdg Z298 Ob 1   0.05  0   0.70 no 2wdg Z45 Ob 1   0.04  0   0.88 no 2wdg Z739 Ob 1   0.11  0   0.71 no 2wdg Z291 Ob 1   0.02  0   0.92 no 2wdg Z218 Ob 1   0.06  0   0.94 no 2wdg Z56 Ob 1   0.05  0   0.57 no 2wdg Z184 Ob 1   0.02  0   0.67 no 2wdg Z42 Ob 1   0.14  0   0.49 no 2wdg Z210 Ob 1   0.02  0   0.78 no 2wdg Z149 Ob 1   0.04  0   0.91 no 2wdg Z213 Ob 1   0.16  0   0.81 no 2wdg Z216 Ob 1   0.01  0   0.69 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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