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 1vs6 1VS6 (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with the antibiotic kasugamyin at 3.5a resolution. this file contains the 50s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes and is List of all 110 Mg2+ binding sites in the PDB structure 1vs6 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 1vs6 B2936 Ob 6   0.91   0.89   0.82 yes 1vs6 B2946 Ob 6   0.87   0.88   1.00 yes 1vs6 B2939 Ob 6   0.97   0.97   0.89 yes 1vs6 B2932 Nb 5   0.69   0.73   0.98 yes 1vs6 B2959 2Nb 6   0.85   0.87   0.73 yes 1vs6 B2948 Oph 6   0.99   0.98   0.93 yes 1vs6 B2962 Oph 6   0.97   0.98   0.83 yes 1vs6 B2972 Oph 6   0.93   0.90   0.99 yes 1vs6 B2934 Oph 6   0.95   0.97   0.97 yes 1vs6 B3010 Oph 6   0.92   0.90   0.83 yes 1vs6 B2930 Oph·Pout 6   0.92   0.94   0.91 yes 1vs6 B2913 Oph·Pout 6   0.94   0.95   0.95 yes 1vs6 B2911 Oph·Pout 6   0.95   0.95   0.96 yes 1vs6 B2950 Oph·Pout 5   0.72   0.77   0.98 yes 1vs6 B2951 Oph·Pout 6   0.91   0.89   0.79 yes 1vs6 B2969 Oph·Pout 6   0.82   0.82   0.99 yes 1vs6 B2965 Oph·Pout 6   0.98   0.97   0.94 yes 1vs6 B2954 Oph·Pout 6   0.99   0.96   0.89 yes 1vs6 B2910 Oph·Pout 6   0.90   0.92   0.99 yes 1vs6 B2905 Oph·2Pout 6   0.86   0.85   0.95 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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