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 2qao 2QAO (3.21Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with neomycin. this file contains the 50s subunit of the second 70s ribosome, with neomycin bound. the entire crystal structure contains two 70s ribosomes and is described in List of all 111 Mg2+ binding sites in the PDB structure 2qao 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 2qao B3351 Ob 6   0.83   0.83   1.00 yes 2qao B3403 Ob 6   0.95   0.92   0.54 yes 2qao B3468 Ob 6   0.93   0.94   0.89 yes 2qao B3099 2Nb 6   0.89   0.96   0.77 yes 2qao B3220 2Nb 6   0.83   0.88   0.72 yes 2qao B3364 Oph 6   0.81   0.81   0.96 yes 2qao B3104 Oph 6   0.86   0.86   0.98 yes 2qao B3251 Oph·Pout 6   0.91   0.89   0.91 yes 2qao B3245 Oph·Pout 6   0.93   0.95   0.91 yes 2qao B3229 Oph·Pout 6   0.94   0.92   0.88 yes 2qao B3159 Oph·Pout 6   0.97   0.93   0.76 yes 2qao B3127 Oph·Pout 6   0.91   0.92   0.92 yes 2qao B3052 Oph·Pout 6   0.95   0.96   0.71 yes 2qao B3474 Oph·Pout 6   0.96   0.96   0.83 yes 2qao B3058 Oph·Pout 6   0.98   0.93   0.80 yes 2qao B3140 Oph·2Pout 6   0.75   0.78   0.89 yes 2qao B3081 Oph·2Pout 6   0.92   0.93   0.95 yes 2qao B3046 Oph·2Pout 6   0.96   0.92   0.87 yes 2qao B3040 Oph·2Pout 6   0.99   0.96   0.85 yes 2qao B3008 Oph·2Pout 6   0.99   0.93   0.96 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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