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 4dv3 4DV3 (3.55Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, c912a, bound with streptomycin List of all 274 Mg2+ binding sites in the PDB structure 4dv3 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 14 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dv3 A1846 4Bout 5   0.74   0.82   0.24 no 4dv3 A1781 other RNA-outer types 6   0.95   0.97   0.25 no 4dv3 A1828 2Bout 6   0.93   0.98   0.27 no 4dv3 A1849 Oph·2Pout 4   0.51   0.43   0.28 no 4dv3 A1674 Oph·Ob 4   0.39   0.34   0.29 no 4dv3 A1823 4Pout 5   0.78   0.79   0.29 no 4dv3 A1692 cis-2Oph·Nb 5   0.34   0.43   0.33 no 4dv3 A1834 2Pout·2Bout 4   0.64   0.63   0.34 no 4dv3 A1836 4Pout 4   0.65   0.64   0.34 no 4dv3 A1847 Pout 3   0.45   0.46   0.34 no 4dv3 A1820 2Pout·Rout 5   0.79   0.79   0.35 no 4dv3 A1831 poly-nuclear Mg2+ site 3   0.48   0.67   0.37 no 4dv3 A1830 3Pout 6   0.97   0.96   0.37 no 4dv3 A1853 Bout 3   0.45   0.70   0.38 no 4dv3 A1637 other RNA-inner types 6   0.41   0.56   0.38 no 4dv3 E201 Mg2+ not bound by RNA 6   0.95   0.98   0.39 no 4dv3 A1854 3Pout 5   0.78   0.79   0.39 no 4dv3 A1829 2Bout 5   0.79   0.79   0.39 no 4dv3 A1857 Pout·3Bout 6   0.95   0.99   0.40 no 4dv3 A1822 2Pout·Bout 6   0.93   0.97   0.40 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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