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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 4dr2



4DR2 (3.25Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with multiple copies of paromomycin molecules bound
List of all 79 Mg2+ binding sites in the PDB structure 4dr2 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 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4dr2 A1757 Ob G:A1370(O6) A2412, A2413, A2414 U:A1351
4dr2 A1655 Ob U:A12(O4) A2100, A2101, A2102, A2103 G:A21, G:A11, G:A22, C:A23
4dr2 A1690 Ob G:A895(O6) A2203, A2204, A2205, A2206 G:A894
4dr2 A1734 Nb G:A324(N7) A2324, A2325, A2326, A2327, A2328 G:A324, G:A326
4dr2 A1726 Nb G:A362(N7) A2299, A2300, A2301, A2302
4dr2 A1761 2Ob U:A1510(O4), G:A1511(O6) A2423, A2424, A2425, A2426 U:A1512, U:A1522, A:A1513, G:A1523, C:A1524
4dr2 A1633 Oph G:A21(OP1) A2053, A2054, A2055, A2056 G:A567, G:A568 G:A567, A:A573
4dr2 A1644 Oph A:A766(OP2) A2071, A2072, A2073, A2074 C:A811, A:A767, C:A812
4dr2 A1763 Oph C:A980(OP1) A2430, A2431, A2432 G:A1220
4dr2 A1695 Oph C:A352(OP2) A2221, A2222, A2223, A2224, A2225 G:A331, C:A352 A:A59, C:A330, G:A354
4dr2 A1694 Oph G:A113(OP1) A2217, A2218, A2219, A2220
4dr2 A1632 Oph A:A937(OP2) A2049, A2050, A2051, A2052 G:A939, A:A938
4dr2 A1741 Oph·Pout A:A53(OP2) A2350, A2351, A2352 A:A353 G:A316
4dr2 A1702 Oph·Pout A:A509(OP2) A2236, A2237, A2238 A:A510 A:A510
4dr2 A1678 Oph·Pout A:A860(OP2) A2174, A2175, A2176 G:A861 G:A861
4dr2 A1656 Oph·Pout C:A307(OP2) A2104, A2105, A2106, A2107 G:A306 G:A309
4dr2 A1649 Oph·Pout A:A547(OP1) A2087, A2088, A2089, A2090 G:A548 G:A402, C:A403
4dr2 A1659 Oph·2Pout G:A588(OP2) A2117, A2118, A2119, A2120 C:A645, G:A644
4dr2 A1708 Oph·2Pout A:A195(OP2) A2253, A2254, A2255, A2256 C:A194, A:A179 U:A180, G:A181, A:A179
4dr2 A1686 Oph·2Pout A:A1110(OP2) A2190, A2191, A2192, A2193 C:A1109, A:A1111 C:A1189, A:A1110, A:A1111, C:A1112

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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