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 1 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 08001 fac-3Oph 6   0.92   0.87   0.97 yes 1yij 08002 cis-2Oph·Ob 6   0.96   0.91   0.96 yes 1yij 08003 fac-3Oph 6   0.95   0.91   0.80 yes 1yij 08004 Oph·Ob 6   0.71   0.92   0.94 yes 1yij 08005 mer-3Oph 6   0.83   0.92   0.96 yes 1yij 08006 poly-nuclear Mg2+ site 6   0.90   0.90   0.99 yes 1yij 08007 mer-3Oph 6   0.93   0.86   0.87 yes 1yij 08008 mer-3Oph 6   0.79   0.88   0.83 yes 1yij 08009 poly-nuclear Mg2+ site 6   0.74   0.85   0.84 yes 1yij 08010 Mg2+ bound by non-RNA 6   0.82   0.83   0.92 yes 1yij 08011 2Nb 6   0.53   0.92   0.84 yes 1yij 08012 Oph·4Pout 6   0.86   0.76   0.91 yes 1yij 08013 cis-2Oph 6   0.75   0.90   0.71 yes 1yij 08014 Oph·Or 6   0.71   0.67   0.99 yes 1yij 08015 trans-2Oph 6   0.76   0.85   0.72 yes 1yij 08016 fac-3Oph 6   0.85   0.86   0.93 yes 1yij 08017 Oph·3Pout 6   0.85   0.84   1.00 yes 1yij 08018 cis-2Oph 6   0.91   0.78   0.94 yes 1yij 08019 Oph·2Pout 6   0.75   0.69   0.88 yes 1yij 08020 Oph·2Pout 6   0.80   0.84   0.87 yes

^# 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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