`

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 3v26




3V26 (3.1Å) -- RIBOSOME : Crystal structure of hpf bound to the 70s ribosome. this pdb entry contains coordinates for the 30s subunit with bound hpf of the 1st ribosome in the asu
List of all 40 Mg2+ binding sites in the PDB structure 3v26 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 2 | « Previous | | 1 | 2
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v26 A1688 Ob G:A1417(O6) A1844, A1845, A1846, A1847 G:A1415 G:A1482, U:A1481
3v26 A1719 Ob G:A21(O6) A1983, A1984, A1985, A1986, A1987 U:A12, G:A22
3v26 A1708 Nb G:A362(N7) A1933, A1934, A1935, L201, L202 G:A361 G:A361
3v26 A1729 Oph G:A1475(OP1) A2025, A2026, A2027, A2028
3v26 A1690 Oph C:A1069(OP2) A1851, A1852, A1853, A1854, A1855
3v26 A1703 Oph A:A766(OP2) A1914, A1915, A1916, A1917, A1918 C:A811, C:A812, U:A813, A:A767
3v26 A1717 Oph G:A21(OP1) A1972, A1973, A1974, A1975, A1976 G:A567, G:A568 G:A567, A:A563, A:A573
3v26 A1706 Oph·Pout A:A270(OP2) A1926, A1927, A1928, A1929 C:A271 G:A251, A:A270, C:A271
3v26 A1700 Oph·Pout G:A903(OP1) A1901, A1902, A1903, A1904, A1905 U:A891 G:A890
3v26 A1702 Oph·2Pout A:A768(OP2) A1909, A1910, A1911, A1912, A1913 C:A805, A:A767 A:A768
3v26 A1693 Oph·3Pout C:A578(OP1) A1868, A1869, A1870, A1871 U:A820, C:A817, G:A576 G:A575
3v26 A1698 Oph·Or A:A509(OP2) A1891, A1892, A1893, A1894 G:A506, C:A507 A:A510
3v26 A1699 Bout A1895, A1896, A1897, A1898, A1899, A1900 C:A48
3v26 A1736 2Bout A2064, A2065, A2066, A2067, A2068, A2069 G:A38, U:A37
3v26 A1737 2Bout A2070, A2071, A2072, A2073, A2074, A2075 G:A42, G:A41
3v26 A1716 2Bout A1967, A1968, A1969, A1970, A1971 G:A1526, G:A1525
3v26 A1715 Rout·2Bout A1962, A1963, A1964, A1965, A1966 U:A870 G:A829, G:A830
3v26 A1718 3Bout A1977, A1978, A1979, A1980, A1981, A1982 G:A191, C:A187, U:A190
3v26 A1720 Rout·4Bout A1988, A1989, A1990, A1991, A1992, A1993 U:A641 G:A592, G:A593, G:A595, G:A594
3v26 A1733 Pout A2047, A2048, A2049, A2050, A2051 G:A1079

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>