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 2otj 2OTJ (2.9Å) -- RIBOSOME : 13-deoxytedanolide bound to the large subunit of haloarcula marismortui List of all 117 Mg2+ binding sites in the PDB structure 2otj 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 5 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 2otj 08112 Nb 5   0.64   0.68   0.74 yes 2otj 08023 cis-2Oph 5   0.96   0.90   0.71 yes 2otj 08100 Pout·2Bout 5   0.79   0.84   0.64 yes 2otj 08089 cis-2Oph 5   0.30   0.37   0.92 no 2otj 08101 Oph·Ob 5   0.23   0.45   0.82 no 2otj 08048 cis-2Oph 5   0.94   0.87   0.79 yes 2otj 08052 cis-2Oph 5   0.58   0.59   0.73 no 2otj A8066 Mg2+ bound by non-RNA 5   0.61   0.78   0.84 yes 2otj 08025 poly-nuclear Mg2+ site 5   0.85   0.60   0.87 yes 2otj 08060 Oph·5Pout 5   0.88   0.68   0.92 yes 2otj 08057 poly-nuclear Mg2+ site 5   0.23   0.84   1.00 no 2otj 08040 Oph·3Pout 5   0.23   0.64   0.88 no 2otj 08067 Mg2+ bound by non-RNA 5   0.40   0.83   0.99 no 2otj 08081 mer-3Oph 5   0.56   0.48   0.84 no 2otj 08106 poly-nuclear Mg2+ site 5   0.26   0.41   0.59 no 2otj 08044 Mg2+ bound by non-RNA 5   0.52   0.88   0.96 yes 2otj 08024 Nb 4   0.10   0.53   0.89 no 2otj 08046 Nb 4   0.37   0.81   0.99 no 2otj 08114 Nb 4   0.34   0.37   0.95 no 2otj 08076 Rout·Bout 4   0.40   0.48   0.74 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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