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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 4dv5




4DV5 (3.68Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, a914g, bound with streptomycin
List of all 29 Mg2+ binding sites in the PDB structure 4dv5 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4dv5 A1602 Ob G:A377(O6) A1901, A1902, A1903, A1904 G:A376
4dv5 A1665 Nb G:A362(N7) A2015, A2016, A2017, A2018 G:A361, G:A362
4dv5 A1686 2Ob G:A1370(O6), G:A1371(O6) A2047, A2048, A2049 U:A1372
4dv5 A1625 2Ob U:A304(O4), G:A305(O6) A1944, A1945, A1946 A:A303, G:A293
4dv5 A1827 Oph C:A972(OP1) A2180, A2181, A2182, A2183 G:A971, U:A1232
4dv5 A1618 Oph·Pout A:A768(OP2) A1932, A1933, A1934, A1935 C:A805 A:A768
4dv5 A1685 Oph·Pout A:A1204(OP2) A2044, A2045, A2046, N201 G:A1048
4dv5 A1649 Oph·Pout C:A352(OP2) A1992, A1993, A1994, A1995, A1996 G:A354 G:A331, C:A330, C:A352 C:A330, A:A59, G:A354
4dv5 A1648 Oph·Pout G:A903(OP1) A1988, A1989, A1990, A1991 U:A891 G:A890
4dv5 A1629 Oph·2Pout G:A588(OP2) A1953, A1954, A1955 C:A589, G:A644
4dv5 A1831 cis-2Oph G:A506(OP1), A:A509(OP2) A2199, A2200, A2201, A2202 A:A510, C:A507
4dv5 A1605 trans-2Oph G:A117(OP2), G:A289(OP2) A1908, A1909, A1910, A1911 A:A116, A:A288 G:A117, U:A118
4dv5 A1774 Bout A2086, A2087, A2088, A2089 G:A1516
4dv5 A1636 Bout A1965, A1966, A1967, A1968 G:A587
4dv5 A1813 Bout A2115, A2116, A2117, P201 C:A137
4dv5 A1824 2Bout A2166, A2167, A2168, A2169 G:A1385, G:A1386
4dv5 A1773 3Bout A2081, A2082, A2083, A2084, A2085 G:A742, G:A741, G:A664
4dv5 A1681 Pout·Bout A2035, A2036, A2037, A2038 A:A415 G:A425
4dv5 A1828 Pout·Rout·Bout A2184, A2185, A2186, A2187 G:A1334 A:A1333 G:A1300
4dv5 A1851 Pout·3Bout A2260, A2261, A2262, A2263, A2264, A2265 A:A583 G:A584, G:A585, U:A757

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/)
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