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 3df1 3DF1 (3.5Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with hygromycin b. this file contains the 30s subunit of the first 70s ribosome, with hygromycin b bound. the entire crystal structure contains two 70s ribosomes. List of all 60 Mg2+ binding sites in the PDB structure 3df1 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 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3df1 A2025 Or 6   0.84   0.83   0.99 yes 3df1 A2355 Ob 6   0.91   0.88   0.91 yes 3df1 A2349 Ob 6   0.82   0.81   0.99 yes 3df1 A2109 Ob 6   0.83   0.82   0.99 yes 3df1 A2103 Nb 6   0.99   0.95   0.99 yes 3df1 A2187 2Nb 6   0.88   0.86   0.89 yes 3df1 A2170 Oph 6   0.84   0.85   0.99 yes 3df1 A2064 Oph 6   0.85   0.86   0.99 yes 3df1 A2176 Oph 6   0.99   0.96   0.97 yes 3df1 A2213 Oph·Pout 6   0.94   0.91   0.99 yes 3df1 A2322 Oph·Pout 6   0.86   0.87   0.99 yes 3df1 A2288 Oph·Pout 6   0.92   0.93   0.97 yes 3df1 A2242 Oph·Pout 6   1.00   0.95   0.97 yes 3df1 A2316 Oph·Pout 6   0.96   0.98   0.98 yes 3df1 A2264 Oph·2Pout 6   0.87   0.88   0.98 yes 3df1 A2306 Oph·2Pout 6   0.83   0.82   0.98 yes 3df1 A2248 Oph·2Pout 6   0.91   0.92   0.99 yes 3df1 A2001 Oph·3Pout 6   0.92   0.93   0.94 yes 3df1 A2164 Oph·3Pout 6   0.82   0.81   0.99 yes 3df1 A2038 Oph·4Pout 6   0.86   0.87   0.92 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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