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 3i56 3I56 (2.9Å) -- RIBOSOME/ANTIBIOTIC : Co-crystal structure of triacetyloleandomcyin bound to the large ribosomal subunit List of all 93 Mg2+ binding sites in the PDB structure 3i56 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 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3i56 08047 Or 5   0.17   0.53   0.76 no 3i56 08088 Nb 6   0.17   0.81   0.79 no 3i56 08077 Nb 6   0.13   0.78   0.57 no 3i56 08017 Nb 4   0.12   0.43   0.85 no 3i56 08036 Nb 4   0.12   0.50   0.90 no 3i56 08090 Nb 6   0.20   0.82   0.89 no 3i56 08059 2Or 6   0.23   0.97   0.93 no 3i56 08078 2Or 5   0.17   0.84   0.87 no 3i56 08076 2Ob 6   0.18   0.78   0.28 no 3i56 08032 2Ob 6   0.15   0.94   0.90 no 3i56 08075 2Ob 6   0.24   0.91   0.76 no 3i56 08080 Ob·Nb 6   0.17   0.76   0.92 no 3i56 08093 2Or·Nb 6   0.23   0.74   0.46 no 3i56 08038 Oph·Pout 2   0.07   0.20   0.58 no 3i56 08065 Oph·Pout 6   0.24   0.75   0.34 no 3i56 08064 Oph·Pout 6   0.24   0.71   0.68 no 3i56 08063 Oph·Pout 6   0.15   0.68   0.70 no 3i56 08029 Oph·2Pout 5   0.22   0.77   0.43 no 3i56 08014 Oph·2Pout 5   0.25   0.46   0.63 no 3i56 08013 Oph·2Pout 6   0.25   0.65   0.22 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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