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 1yij 1YIJ (2.6Å) -- RIBOSOME : Crystal structure of telithromycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui List of all 116 Mg2+ binding sites in the PDB structure 1yij 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 3 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1yij 08075 2Or 6   0.49   0.83   0.83 no 1yij 08046 Nb 4   0.28   0.79   0.84 no 1yij 08009 poly-nuclear Mg2+ site 6   0.74   0.85   0.84 yes 1yij 08082 Oph·2Pout 5   0.26   0.35   0.84 no 1yij 08098 Nb 6   0.34   0.71   0.84 no 1yij 08011 2Nb 6   0.53   0.92   0.84 yes 1yij 08034 cis-2Oph 6   0.90   0.91   0.84 yes 1yij 08023 cis-2Oph 6   0.90   0.93   0.84 yes 1yij 08116 2Or·Nb 6   0.33   0.79   0.85 no 1yij 08050 Oph·Pout 2   0.13   0.22   0.85 no 1yij B8056 Mg2+ bound by non-RNA 6   0.98   0.91   0.85 yes 1yij 08097 2Ob 6   0.32   0.89   0.85 no 1yij 08074 cis-2Oph 6   0.87   0.88   0.85 yes 1yij 08115 poly-nuclear Mg2+ site 6   0.37   0.80   0.86 no 1yij 08031 poly-nuclear Mg2+ site 5   0.75   0.71   0.86 yes 1yij 08033 fac-3Oph·Ob 6   0.97   0.95   0.86 yes 1yij 08058 poly-nuclear Mg2+ site 6   0.99   0.89   0.86 yes 1yij 08020 Oph·2Pout 6   0.80   0.84   0.87 yes 1yij 08007 mer-3Oph 6   0.93   0.86   0.87 yes 1yij 08045 Oph·2Pout 5   0.44   0.57   0.87 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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