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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 4dr6



4DR6 (3.3Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, near-cognate transfer rna anticodon stem-loop mismatched at the first codon position and streptomycin bound
List of all 48 Mg2+ binding sites in the PDB structure 4dr6 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
4dr6 A1717 Ob G:A258(O6) A2291, A2292, A2293, A2294 G:A266 G:A257
4dr6 A1709 Ob G:A1370(O6) A2270, A2271, A2272 U:A1351
4dr6 A1688 Nb G:A362(N7) A2214, A2215, A2216, A2217 G:A361, G:A362
4dr6 A1624 Oph A:A766(OP2) A2062, A2063, A2064, A2065 A:A767, U:A813, C:A812, C:A811
4dr6 A1615 Oph G:A21(OP1) A2045, A2046, A2047 G:A568 A:A573
4dr6 A1614 Oph A:A937(OP2) A2041, A2042, A2043, A2044 G:A939, A:A937, A:A938
4dr6 A1666 Oph·Pout C:A352(OP2) A2163, A2164, A2165, A2166, A2167 G:A354 G:A331, C:A352 A:A59, C:A330, G:A354
4dr6 A1620 Oph·Pout A:A768(OP2) A2053, A2054, A2055, A2056 C:A805 A:A768, G:A769
4dr6 A1698 Oph·Pout G:A1094(OP1) A2237, A2238, A2239, A2240 G:A1068 G:A1387, C:A1388
4dr6 A1699 Oph·Pout A:A53(OP2) A2241, A2242, A2243 A:A353
4dr6 A1677 Oph·2Pout A:A195(OP2) A2187, A2188, A2189, A2190 C:A178, C:A194 A:A179, U:A180, G:A181
4dr6 A1721 Oph·2Pout A:A794(OP1) A2302, A2303, A2304, A2305 A:A782, C:A783 C:A1515 C:A1515
4dr6 A1641 Oph·3Pout C:A578(OP1) A2109, A2110, A2111, A2112 U:A820, G:A576, C:A817
4dr6 A1635 Oph·3Pout G:A588(OP2) A2094, A2095, A2096, A2097 G:A644, C:A645, C:A589
4dr6 A1720 Oph·Ob A:A1238(OP2) C:A1335(O2) A2299, A2300, A2301
4dr6 A1604 cis-2Oph C:A749(OP2), G:A750(OP2) A2011, A2012, A2013, A2014 G:A752
4dr6 A1724 cis-2Oph A:A964(OP1), U:A1199(OP1) A2310, A2311, A2312
4dr6 A1700 cis-2Oph C:A1054(OP2), G:A1197(OP2) A2244, A2245, A2246 G:A1053 G:A1197
4dr6 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A2015, A2016, A2017, A2018 A:A116, A:A288 G:A117
4dr6 A1648 Bout A2123, A2124, A2125, A2126 G:A587

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/)
For any help please contact <dust@iwonka.med.virginia.edu>