MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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List of Mg2+ binding sites in structure 4dv1

4DV1 (3.85Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u20g, bound with streptomycin
List of all 28 Mg2+ binding sites in the PDB structure 4dv1 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
4dv1 A1602 Ob G:A377(O6) A1901, A1902, A1903, A1904 G:A376
4dv1 A1684 Ob G:A1370(O6) A2056, A2057, A2058 G:A1371, U:A1372
4dv1 A1665 Nb G:A362(N7) A2022, A2023, A2024, A2025 G:A361 G:A361
4dv1 A1613 Oph G:A21(OP1) A1930, A1931, A1932 A:A563, A:A573
4dv1 A1617 Oph·Pout A:A768(OP2) A1937, A1938, A1939, A1940 C:A805 A:A768
4dv1 A1649 Oph·Pout C:A352(OP2) A1999, A2000, A2001, A2002, A2003 G:A354 G:A331, C:A352 A:A59, G:A354
4dv1 A1677 Oph·Pout G:A1197(OP2) A2037, A2038, A2039 C:A1054 G:A1053 G:A1198, U:A1199
4dv1 A1628 Oph·2Pout G:A588(OP2) A1959, A1960, A1961 G:A644, C:A645
4dv1 A1605 Oph·3Pout G:A117(OP2) A1908, A1909, A1910, A1911 A:A116, G:A289, A:A288 G:A117, U:A118
4dv1 A1796 2Bout A2132, A2133, A2134, A2135 G:A1186, G:A1185
4dv1 A1764 4Bout A2091, A2092, A2093, A2094, A2095, A2096 G:A664, G:A741, G:A742, G:A666
4dv1 A1635 Pout A1971, A1972, A1973, A1974 U:A646
4dv1 A1648 Pout·Rout A1995, A1996, A1997, A1998 G:A903 G:A890
4dv1 A1766 Pout·Rout A2101, A2102, A2103, A2104, A2105 A:A777 G:A713
4dv1 A1822 Pout·Rout·2Bout A2244, A2245, A2246, A2247, A2248 C:A1303 G:A1331 G:A1305, G:A1304
4dv1 A1745 Pout·Rout·2Bout A2080, A2081, A2082, A2083 A:A642 U:A641 G:A595, G:A593
4dv1 A1810 Pout·4Bout A2206, A2207, A2208, A2209, A2210, A2211 A:A766 U:A813, C:A811, C:A812, A:A767
4dv1 A1823 2Pout·Bout A2249, A2250, A2251, A2252, A2253 G:A1224, G:A951 A:A977
4dv1 A1747 2Pout·2Bout A2087, A2088, A2089, A2090 A:A608, A:A607 A:A609, G:A610
4dv1 A1611 3Pout A1923, A1924, A1925, A1926, A1927 G:A617, C:A620, A:A621

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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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