`

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 4dr1



4DR1 (3.6Å) -- RIBOSOME : Crystal structure of the apo 30s ribosomal subunit from thermus thermophilus (hb8)
List of all 23 Mg2+ binding sites in the PDB structure 4dr1 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
4dr1 A1711 Ob G:A1370(O6) A2082, A2083, A2084 G:A1371, U:A1372
4dr1 A1688 Nb G:A362(N7) A2044, A2045, A2046, L301
4dr1 A1695 Nb G:A324(N7) A2054, A2055, T201, T202
4dr1 A1615 Oph A:A937(OP2) A1935, A1936, A1937, A1938 G:A939, A:A937, A:A938
4dr1 A1616 Oph G:A21(OP1) A1939, A1940, A1941 G:A568 A:A573
4dr1 A1623 Oph A:A766(OP2) A1951, A1952, A1953, A1954 U:A813, C:A812, C:A811
4dr1 A1635 Oph·Pout G:A588(OP2) A1964, A1965, A1966, A1967 C:A589
4dr1 A1665 Oph·Pout C:A352(OP2) A2019, A2020, A2021, A2022 G:A354 G:A331, C:A352 A:A59, G:A354
4dr1 A1660 Oph·2Pout A:A1110(OP2) A2011, A2012, A2013 C:A1109, A:A1111 C:A1189, A:A1111
4dr1 A1671 Oph·2Pout A:A509(OP2) A2024, A2025, A2026 A:A510, G:A506 A:A510
4dr1 A1641 Oph·2Pout C:A578(OP1) A1980, A1981, A1982, A1983 U:A820, G:A576
4dr1 A1606 Oph·3Pout G:A117(OP2) A1909, A1910, A1911, A1912 A:A116, G:A289, A:A288 G:A117
4dr1 A1633 Oph·4Pout U:A560(OP2) A1960, A1961, A1962, A1963 C:A562, G:A557, G:A558, A:A563
4dr1 A1724 trans-2Oph A:A782(OP1), A:A794(OP1) A2103, A2104, A2105 C:A783 C:A1515 C:A1515
4dr1 A1612 2Bout A1922, A1923, A1924, A1925, A1926 G:A1526, G:A1525
4dr1 A1640 Pout·2Bout A1975, A1976, A1977, A1978, A1979 A:A583 G:A584, G:A585
4dr1 A1705 Pout·2Bout A2070, A2071, A2072, A2073 A:A1360 C:A980, A:A1360
4dr1 A1710 2Pout A2078, A2079, A2080, A2081 A:A1204, U:A1049
4dr1 A1608 2Pout·Bout A1913, A1914, A1915, A1916 C:A651, U:A751 G:A752
4dr1 A1814 2Pout·4Bout A2126, A2127, A2128, A2129 U:A264, G:A265 G:A190, G:A260, U:A261, G:A259

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>