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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 4dv7



4DV7 (3.29Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, a915g, bound with streptomycin
List of all 41 Mg2+ binding sites in the PDB structure 4dv7 in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4dv7 A1872 3Bout A2284, A2285, A2286, A2287 G:A837, G:A838, C:A840
4dv7 A1782 3Bout A2088, A2089, A2090, A2091, A2092 G:A664, G:A742, G:A741
4dv7 A1835 3Bout A2144, A2145, A2146, A2147, A2148 G:A853, G:A854, G:A852
4dv7 A1871 Pout·2Bout A2278, A2279, A2280, A2281, A2282, A2283 A:A583 G:A584, G:A585
4dv7 A1839 Pout·3Bout A2165, A2166, A2167, A2168, A2169, A2170 A:A119 G:A286, U:A287, G:A285
4dv7 A1846 Pout·4Bout A2201, A2202, A2203, A2204, A2205, A2206 A:A766 U:A813, C:A812, A:A767, C:A811
4dv7 A1866 Pout·5Bout A2250, A2251, A2252, A2253, A2254, A2255 G:A266 G:A257, G:A258, U:A256, G:A266, G:A255
4dv7 A1842 2Pout A2181, A2182, A2183, A2184 G:A576, G:A577
4dv7 A1844 2Pout·Rout A2192, A2193, A2194, A2195, A2196 C:A972, C:A1366 G:A971
4dv7 A1870 2Pout·2Bout A2272, A2273, A2274, A2275, A2276, A2277 G:A391, C:A390 G:A392, G:A391
4dv7 A1865 2Pout·2Bout A2245, A2246, A2247, A2248, A2249 G:A1224, G:A951 A:A974, A:A977
4dv7 A1864 2Pout·Rout·2Bout A2240, A2241, A2242, A2243, A2244 C:A1303, U:A1301 G:A1331 G:A1304, G:A1305
4dv7 A1869 2Pout·3Bout A2266, A2267, A2268, A2269, A2270, A2271 A:A151, A:A152 G:A168, G:A166, G:A167
4dv7 A1607 3Pout A1912, A1913, A1914, A1915 C:A651, U:A652, U:A751
4dv7 A1785 3Pout A2100, A2101, A2102, A2103, A2104, A2105 C:A1103, A:A1101, C:A1100
4dv7 A1611 3Pout·Bout A1923, A1924, A1925, A1926, A1927 G:A617, C:A620, A:A621 G:A617
4dv7 A1863 3Pout·2Bout A2234, A2235, A2236, A2237, A2238, A2239 G:A858, C:A868, C:A857 G:A858, G:A869
4dv7 A1862 3Pout·2Bout A2228, A2229, A2230, A2231, A2232, A2233 G:A581, U:A580, G:A758 G:A758, G:A581
4dv7 A1829 4Pout·Bout A2115, A2116, A2117, A2118, A2119, A2120 C:A150, A:A151, G:A168, G:A167 G:A168
4dv7 A1834 5Pout A2138, A2139, A2140, A2141, A2142, A2143 C:A330, C:A328, C:A314, A:A315, A:A329

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/)
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