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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 4dr4



4DR4 (3.97Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, cognate transfer rna anticodon stem-loop and multiple copies of paromomycin molecules bound
List of all 68 Mg2+ binding sites in the PDB structure 4dr4 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
4dr4 A1760 Ob G:A1370(O6) A2324, A2325, A2326 G:A1371, C:A1352
4dr4 A1737 Nb G:A324(N7) A2259, A2260, A2261, A2262 G:A324
4dr4 A1729 Nb G:A362(N7) A2244, A2245, A2246, L302 G:A361, G:A362
4dr4 A1644 Oph A:A766(OP2) A2058, A2059, A2060, A2061 C:A812
4dr4 A1634 Oph G:A21(OP1) A2042, A2043, A2044 G:A567, G:A568 A:A563
4dr4 A1766 Oph C:A980(OP1) A2341, A2342, A2343 G:A1220
4dr4 A1744 Oph·Pout A:A53(OP2) A2278, A2279, A2280 A:A353
4dr4 A1633 Oph·Pout A:A937(OP2) A2038, A2039, A2040, A2041 A:A938 G:A939, A:A937, A:A938
4dr4 A1622 Oph·Pout G:A750(OP2) A2010, A2011, A2012, A2013 C:A749 G:A752
4dr4 A1743 Oph·Pout G:A1094(OP1) A2274, A2275, A2276, A2277 G:A1068 G:A1387, C:A1388 U:A1091
4dr4 A1717 Oph·Pout U:A182(OP1) A2217, A2218, A2219, A2220 G:A183 G:A181
4dr4 A1748 Oph·Pout G:A1197(OP2) A2288, A2289, A2290, A2291 C:A1054 G:A1197, G:A1198, U:A1199
4dr4 A1698 Oph·Pout C:A352(OP2) A2180, A2181, A2182, A2183, A2184 G:A354 G:A331, C:A352 A:A59, G:A354, C:A330
4dr4 A1640 Oph·Pout A:A768(OP2) A2049, A2050, A2051, A2052 C:A805 A:A768
4dr4 A1711 Oph·2Pout A:A195(OP2) A2210, A2211, A2212, A2213 A:A179, C:A194 U:A180, G:A181
4dr4 A1705 Oph·2Pout A:A509(OP2) A2196, A2197, A2198 A:A510, G:A506 C:A508 A:A510
4dr4 A1697 Oph·2Pout G:A113(OP1) A2176, A2177, A2178, A2179 C:A308, C:A390
4dr4 A1689 Oph·2Pout A:A1110(OP2) A2153, A2154, A2155, C301 A:A1111, C:A1109 A:A1111, C:A1189
4dr4 A1667 Oph·3Pout C:A578(OP1) A2116, A2117, A2118, A2119 U:A820, G:A576, C:A817
4dr4 A1660 Oph·3Pout G:A588(OP2) A2097, A2098, A2099, A2100 G:A644, C:A645, C:A589

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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