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 4tp7 4TP7 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to virginiamycin m1. this file contains the 50s subunit of the second 70s ribosome with virginiamycin m1 bound. List of all 168 Mg2+ binding sites in the PDB structure 4tp7 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 4 of 9 | « 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 4tp7 A3005 Oph·Pout 6   0.83   0.84   0.77 yes 4tp7 A3139 Ob 1   0.09  0   0.78 no 4tp7 A3003 3Pout·Rout·4Bout 6   0.74   1.00   0.78 yes 4tp7 A3009 Oph·3Pout 6   0.83   0.83   0.78 yes 4tp7 A3141 Oph 1   0.05  0   0.78 no 4tp7 A3041 4Pout·Bout 4   0.67   0.65   0.79 yes 4tp7 A3033 cis-2Oph 6   0.70   0.70   0.79 yes 4tp7 A3035 mer-3Oph 6   0.55   0.85   0.79 yes 4tp7 A3093 3Bout 6   0.74   0.99   0.79 yes 4tp7 A3060 Oph·2Pout 6   0.83   0.82   0.79 yes 4tp7 A3101 Oph·Pout 6   0.90   0.92   0.79 yes 4tp7 2101 Pout·2Bout 6   0.74   0.99   0.79 yes 4tp7 A3078 Oph·Pout 5   0.71   0.75   0.79 yes 4tp7 A3049 3Pout·2Bout 5   0.81   0.81   0.79 yes 4tp7 A3034 Oph·Pout 6   0.87   0.89   0.79 yes 4tp7 A3070 Oph·3Pout 6   0.87   0.87   0.80 yes 4tp7 A3090 Ob 6   0.83   0.83   0.80 yes 4tp7 A3075 cis-2Oph 6   0.81   0.89   0.80 yes 4tp7 A3016 2Pout·Rout·Bout 6   0.74   0.99   0.80 yes 4tp7 A3012 4Pout 6   0.74   0.99   0.81 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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