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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 4dv6




4DV6 (3.3Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, a915g
List of all 43 Mg2+ binding sites in the PDB structure 4dv6 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 3 | « Previous | | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4dv6 A1687 Or C:A1054(O5') A2047, A2048, A2049 G:A1198, C:A1054, G:A1197 U:A1196
4dv6 A1774 Ob G:A610(O6) A2097, A2098, A2099, A2100 A:A608, A:A607 A:A609
4dv6 A1702 Ob G:A258(O6) A2077, A2078, A2079, A2080 G:A266 G:A257
4dv6 A1634 Nb G:A758(N7) A1965, A1966, A1967 U:A757, G:A758 G:A581
4dv6 A1681 Nb G:A324(N7) A2035, A2036, A2037, A2038 G:A326
4dv6 A1834 Nb A:A353(N7) A2283, A2284, A2285, A2286 A:A53, A:A353 G:A316
4dv6 A1674 Nb G:A362(N7) A2025, A2026, A2027, L302 G:A361, G:A362 G:A361
4dv6 A1621 Oph A:A766(OP2) A1947, A1948, A1949, A1950 A:A767, C:A812, C:A811
4dv6 A1656 Oph·Pout C:A352(OP2) A2004, A2005, A2006, A2007 G:A354 G:A331, C:A352 A:A59, C:A330, G:A354
4dv6 A1613 Oph·Pout A:A937(OP2) A1934, A1935, A1936, A1937 A:A938 A:A937, A:A938, G:A939
4dv6 A1652 Oph·2Pout A:A1110(OP2) A1996, A1997, A1998 C:A1109, A:A1111 C:A1189, A:A1111
4dv6 A1631 Oph·3Pout G:A588(OP2) A1957, A1958, A1959, A1960 C:A645, G:A644, C:A589
4dv6 A1629 Oph·4Pout U:A560(OP2) A1953, A1954, A1955, A1956 C:A562, A:A563, G:A557, G:A558 A:A559 G:A566
4dv6 A1706 cis-2Oph A:A782(OP1), A:A794(OP1) A2083, A2084, A2085
4dv6 A1826 cis-2Oph U:A13(OP1), U:A14(OP2) A2253, A2254, A2255, A2256 A:A914
4dv6 A1660 trans-2Oph G:A506(OP1), A:A509(OP2) A2009, A2010, A2011 A:A510 A:A510
4dv6 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1909, A1910, A1911, A1912 A:A116, A:A288 G:A117
4dv6 A1692 Bout A2057, A2058, A2059, A2060 G:A700
4dv6 A1643 Bout A1982, A1983, A1984, A1985 G:A587
4dv6 A1797 Bout A2124, A2125, D403, D404 U:A5

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].


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