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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 3v22




3V22 (3Å) -- RIBOSOME : Crystal structure of rmf bound to the 70s ribosome. this pdb entry contains coordinates for the 30s subunit with bound rmf of the 1st ribosome in the asu
List of all 18 Mg2+ binding sites in the PDB structure 3v22 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"
Page 1 of 1
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v22 A1693 Or·Ob C:A280(O2') A1894, A1895, A1896, Q201 G:A281
3v22 A1694 Oph G:A21(OP1) A1897, A1898, A1899, A1900, A1901 G:A568, G:A567 A:A563, G:A567, A:A573
3v22 A1692 Oph·Pout A:A766(OP2) A1889, A1890, A1891, A1892, A1893 A:A767 C:A811, C:A812, U:A813, A:A767
3v22 A1688 Oph·2Pout G:A903(OP1) A1870, A1871, A1872, A1873 U:A1512, C:A904
3v22 A1683 Oph·2Pout C:A1069(OP2) A1847, A1848, A1849, A1850 C:A1389, U:A1070
3v22 A1685 Oph·3Pout G:A576(OP1) A1856, A1857, A1858, A1859, A1860 A:A815, G:A575, G:A577
3v22 A1691 Oph·3Pout A:A768(OP2) A1884, A1885, A1886, A1887, A1888 U:A804, C:A805, A:A767 A:A768, G:A769
3v22 A1703 Oph·3Pout A:A315(OP1) A1928, A1929, A1930, A1931 G:A318, G:A316, G:A317 G:A318, G:A319
3v22 A1705 Oph·4Pout U:A560(OP2) A1935, A1936, A1937, A1938 C:A562, A:A563, G:A557, G:A558 A:A559 G:A566
3v22 A1689 trans-2Oph G:A588(OP2), G:A644(OP1) A1874, A1875, A1876, A1877 C:A589, C:A645 G:A587
3v22 A1696 3Bout A1904, A1905, A1906, A1907 G:A46, G:A394, C:A366
3v22 A1686 Pout A1861, A1862, A1863, A1864, A1865, A1866 C:A770
3v22 A1684 Pout·Bout A1851, A1852, A1853, A1854, A1855 G:A1079 G:A1077
3v22 A1706 Pout·3Bout A1939, A1940, A1941, A1942, A1943, A1944 A:A781 G:A799, G:A800, G:A798
3v22 A1690 2Pout·2Bout A1878, A1879, A1880, A1881, A1882, A1883 G:A803, U:A804 U:A772, G:A771
3v22 A1700 2Pout·2Bout A1916, A1917, A1918, A1919 C:A893, G:A894 G:A895, G:A894
3v22 A1698 3Pout A1910, A1911, A1912, A1913 C:A578, C:A817, G:A576
3v22 A1707 4Pout A1945, A1946, A1947, A1948, A1949 A:A16, U:A13, U:A14, G:A15

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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