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 4ji4

4JI4 (3.69Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of 30s ribosomal subunit from thermus thermophilus
List of all 20 Mg2+ binding sites in the PDB structure 4ji4 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
4ji4 A1713 Ob G:A258(O6) A2086, A2087, A2088, A2089 G:A266 G:A259, G:A257
4ji4 A1686 Nb G:A362(N7) A2034, A2035, A2036, A2037 G:A361, G:A362 G:A361
4ji4 A1691 Nb G:A324(N7) A2043, A2044, A2045, A2046 G:A324
4ji4 A1706 Ob·Nb G:A1370(O6) A2073, A2074, A2075 U:A1372
4ji4 A1614 Oph A:A937(OP2) A1935, A1936, A1937, A1938 G:A939, A:A938
4ji4 A1615 Oph G:A21(OP1) A1939, A1940, A1941 G:A567, A:A573
4ji4 A1622 Oph A:A766(OP2) A1948, A1949, A1950, A1951 C:A812, U:A813, C:A811
4ji4 A1663 Oph·Pout C:A352(OP2) A2009, A2010, A2011, A2012 G:A354 C:A330, G:A331, C:A352 A:A59, G:A354
4ji4 A1633 Oph·2Pout G:A588(OP2) A1957, A1958, A1959, A1960 G:A644, C:A589
4ji4 A1658 Oph·2Pout A:A1110(OP2) A2002, A2003, C401 A:A1111, C:A1109 A:A1111, C:A1189
4ji4 A1606 Oph·3Pout G:A117(OP2) A1909, A1910, A1911, A1912 A:A116, G:A289, A:A288 G:A117, U:A118
4ji4 A1631 Oph·3Pout U:A560(OP1) A1953, A1954, A1955, A1956 A:A563, G:A558, C:A562 A:A559
4ji4 A1669 Oph·3Pout A:A509(OP2) A2014, A2015, A2016 A:A510, G:A506, C:A507 A:A510
4ji4 A1717 trans-2Oph A:A782(OP1), A:A794(OP1) A2092, A2093, A2094 C:A783 C:A1515
4ji4 A1611 2Bout A1922, A1923, A1924, A1925, A1926 G:A1526, G:A1525
4ji4 A1638 Pout·2Bout A1968, A1969, A1970, A1971, Q301 A:A583 G:A584, G:A585
4ji4 A1701 Pout·3Bout A2061, A2062, A2063, A2064 A:A1360 C:A980, C:A979, A:A1360
4ji4 A1608 3Pout A1913, A1914, A1915, A1916 U:A652, C:A651, U:A751
4ji4 A1612 3Pout A1927, A1928, A1929, A1930, A1931 G:A617, C:A620, A:A621
4ji4 A1652 4Pout A1994, A1995, A1996, A1997 G:A15, A:A16, U:A13, U:A14

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>