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 4too 4TOO (3Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to linopristin. this file contains the 50s subunit of the second 70s ribosome with linopristin bound. List of all 169 Mg2+ binding sites in the PDB structure 4too 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 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 4too A3022 Ob 6   0.88   0.88   0.99 yes 4too B202 Ob 6   0.89   0.90   0.98 yes 4too A3158 Ob 1   0.02  0   0.83 no 4too A3101 Ob 6   0.86   0.86   0.74 yes 4too A3089 Ob 6   0.82   0.83   0.64 yes 4too A3139 Ob 1   0.03  0   0.69 no 4too A3133 Ob 6   0.86   0.87   0.93 yes 4too A3072 Nb 6   0.81   0.84   0.68 yes 4too A3045 Ob·Nb 6   0.81   0.78   0.84 yes 4too A3020 2Nb 6   0.77   0.72   0.87 yes 4too A3148 Oph 1   0.02  0   0.69 no 4too A3146 Oph 1   0.10  0   0.56 no 4too A3143 Oph 1   0.01  0   0.62 no 4too A3159 Oph 1   0.02  0   0.75 no 4too A3141 Oph 1   0.07  0   0.97 no 4too A3144 Oph 1   0.04  0   0.97 no 4too A3140 Oph 1   0.12  0   0.67 no 4too B201 Oph 5   0.71   0.70   0.94 yes 4too A3003 Oph 6   0.89   0.89   1.00 yes 4too A3138 Oph 2   0.12   0.10   0.58 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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