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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 4dv7



4DV7 (3.29Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, a915g, bound with streptomycin
List of all 41 Mg2+ binding sites in the PDB structure 4dv7 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
4dv7 A1764 Ob G:A610(O6) A2083, A2084, A2085, A2086 A:A608, A:A609 A:A609
4dv7 A1687 Ob G:A1370(O6) A2055, A2056, A2057 U:A1372
4dv7 A1667 Nb G:A362(N7) A2021, A2022, A2023, A2024 G:A361, G:A362
4dv7 A1626 2Ob U:A304(O4), G:A305(O6) A1951, A1952, A1953 G:A293
4dv7 A1613 Oph G:A21(OP1) A1930, A1931, A1932 A:A563, G:A567, A:A573
4dv7 A1680 Oph·Pout G:A1197(OP2) A2036, A2037, A2038 C:A1054 G:A1198, U:A1199, G:A1197
4dv7 A1651 Oph·Pout C:A352(OP2) A1998, A1999, A2000, A2001, A2002 G:A354 G:A331, C:A352 A:A59, C:A330, G:A354
4dv7 A1845 Oph·Pout G:A1334(OP2) A2197, A2198, A2199, A2200 A:A1333 G:A1300
4dv7 A1630 Oph·Pout G:A588(OP2) A1959, A1960, A1961 G:A644
4dv7 A1618 Oph·Pout A:A768(OP2) A1936, A1937, A1938, A1939 C:A805 A:A768, G:A769
4dv7 A1650 Oph·2Pout G:A903(OP1) A1994, A1995, A1996, A1997 U:A891, C:A904 G:A890
4dv7 A1848 Oph·3Pout G:A506(OP1) A2213, A2214, A2215, A2216, A2217 C:A507, A:A509, A:A510 C:A508 A:A510
4dv7 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117
4dv7 A1840 Bout A2171, A2172, A2173, A2174, A2175 G:A126
4dv7 A1867 Bout A2256, A2257, A2258, A2259, A2260 G:A700
4dv7 A1832 2Bout A2128, A2129, A2130, A2131 G:A1185, G:A1186
4dv7 A1841 2Bout A2176, A2177, A2178, A2179, A2180 G:A1386, G:A1385
4dv7 A1602 3Bout A1901, A1902, A1903, A1904 C:A372, U:A375, G:A376
4dv7 A1872 3Bout A2284, A2285, A2286, A2287 G:A837, G:A838, C:A840
4dv7 A1830 3Bout A2121, A2122, P201, P202 C:A137, G:A138, G:A226

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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