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 3oas 3OAS (3.25Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the e. coli ribosome bound to telithromycin. this file contains the 50s subunit of the second 70s ribosome. List of all 137 Mg2+ binding sites in the PDB structure 3oas 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 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3oas A3003 Or 5   0.60   0.63   0.74 yes 3oas A2999 Ob 6   0.87   0.85   0.87 yes 3oas A3031 Ob 6   0.84   0.84   0.92 yes 3oas B590 Ob 6   0.84   0.83   0.97 yes 3oas A3013 Ob 5   0.70   0.70   1.00 yes 3oas A2926 Ob 6   0.83   0.83   1.00 yes 3oas A2932 Nb 5   0.69   0.67   0.65 yes 3oas A3010 2Or 5   0.42   0.80   0.99 no 3oas A2949 2Nb 6   0.75   0.77   0.91 yes 3oas A2924 2Nb 6   0.78   0.77   0.92 yes 3oas A2957 Oph 6   0.93   0.94   0.93 yes 3oas A2940 Oph 6   0.85   0.85   0.83 yes 3oas A2922 Oph 5   0.72   0.70   0.97 yes 3oas A2986 Oph 6   0.86   0.85   0.99 yes 3oas A2910 Oph 6   0.83   0.82   0.87 yes 3oas A2913 Oph 6   0.82   0.82   0.50 yes 3oas A2931 Oph·Pout 6   0.83   0.82   0.65 yes 3oas A2917 Oph·Pout 6   0.83   0.83   0.74 yes 3oas A2909 Oph·Pout 6   0.86   0.85   0.98 yes 3oas A2908 Oph·Pout 6   0.83   0.83   0.82 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].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>