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 3uz7 3UZ7 (3Å) -- RIBOSOME : Crystal structure analysis of ribosomal decoding. this entry contains the 30s ribosomal subunit of the second 70s molecule in the asymmetric unit for the cognate trna-tyr complex. List of all 261 Mg2+ binding sites in the PDB structure 3uz7 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 10 of 14 | « Previous | Next » | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3uz7 A1821 Oph 1   0.03  0   0.78 no 3uz7 A1824 Oph 1   0.04  0   0.81 no 3uz7 A1827 Oph 1   0.04  0   0.86 no 3uz7 A1862 Ob 1   0.01  0   0.97 no 3uz7 A1865 Oph 1   0.02  0   0.88 no 3uz7 A1874 Ob 1   0.01  0   0.67 no 3uz7 A1887 Oph 1   0.02  0   0.88 no 3uz7 A1897 Oph 1   0.06  0   0.97 no 3uz7 A1929 poly-nuclear Mg2+ site 1   0.02  0   0.70 no 3uz7 A1966 Oph 1   0.04  0   0.81 no 3uz7 A1999 Ob 1   0.03  0   0.90 no 3uz7 A2001 Ob 1   0.02  0   0.88 no 3uz7 A2027 Nb 1   0.01  0   0.93 no 3uz7 A2038 Ob 1   0.02  0   0.93 no 3uz7 A2041 Oph 1   0.02  0   0.72 no 3uz7 A2048 Nb 1   0.01  0   0.90 no 3uz7 A2055 Oph 1   0.01  0   0.79 no 3uz7 A2092 Nb 1   0.01  0   0.86 no 3uz7 A2098 Or 1   0.02  0   0.96 no 3uz7 A2124 Nb 1   0.06  0   0.67 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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