`

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 4dv0



4DV0 (3.85Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u20g
List of all 29 Mg2+ binding sites in the PDB structure 4dv0 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
4dv0 A1688 Ob G:A1370(O6) A2059, A2060, A2061 G:A1371
4dv0 A1669 Nb G:A362(N7) A2023, A2024, A2025, A2026 G:A361 G:A361
4dv0 A1806 Nb A:A353(N7) A2199, A2200, A2201, A2202 A:A353, A:A53
4dv0 A1620 Oph A:A766(OP2) A1948, A1949, A1950, A1951 C:A812, U:A813, C:A811
4dv0 A1627 Oph·Pout U:A560(OP2) A1954, A1955, A1956, A1957 A:A563 A:A559 G:A566
4dv0 A1652 Oph·Pout C:A352(OP2) A2002, A2003, A2004, A2005 G:A354 G:A331, C:A352 A:A59, G:A354
4dv0 A1613 Oph·Pout A:A937(OP2) A1934, A1935, A1936, A1937 A:A938 A:A938, G:A939
4dv0 A1648 Oph·2Pout A:A1110(OP2) A1995, A1996, A1997 C:A1109, A:A1111 C:A1189, A:A1111
4dv0 A1628 Oph·2Pout G:A588(OP2) A1958, A1959, A1960, A1961 G:A644, C:A589
4dv0 A1634 Oph·3Pout C:A578(OP1) A1972, A1973, A1974, A1975 U:A820, G:A576, C:A817
4dv0 A1605 cis-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117
4dv0 A1656 trans-2Oph G:A506(OP1), A:A509(OP2) A2007, A2008, A2009 A:A510 A:A510
4dv0 A1698 trans-2Oph A:A782(OP1), A:A794(OP1) A2079, A2080, A2081 C:A783 C:A1515 C:A1515
4dv0 A1639 Bout A1981, A1982, A1983, A1984 G:A587
4dv0 A1610 Bout A1922, A1923, A1924, A1925 G:A1526
4dv0 A1685 Bout A2052, A2053, A2054, A2055 G:A700
4dv0 A1780 4Bout A2103, A2104, A2105, A2106 G:A664, G:A666, U:A740, G:A741
4dv0 J202 Pout A2229, I201, J301, J302, J303, N201 C:A1189
4dv0 A1684 Pout·4Bout A2048, A2049, A2050, A2051 A:A1360 C:A980, C:A979, A:A1360, G:A1361
4dv0 A1818 2Pout·Rout A2244, A2245, M303, M304, M305 C:A1322, A:A1225 G:A1224

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>