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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 2qbd



2QBD (3.3Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with ribosome recycling factor (rrf). this file contains the 30s subunit of the first 70s ribosome. the entire crystal structure contains two 70s ribosomes and is described in
List of all 59 Mg2+ binding sites in the PDB structure 2qbd 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
2qbd A2355 Ob G:A1417(O6) A2356, A2357, A2358, A2359, A2360 G:A1415 G:A1482, G:A1416
2qbd A2199 Ob G:A1370(O6) A2200, A2201, A2202, A2203, A2204 G:A1371, U:A1372, U:A1351
2qbd A2109 Ob G:A1050(O6) A2110, A2111, A2112, A2113, A2114 G:A1048, G:A1207, C:A1051
2qbd A2103 Nb G:A362(N7) A2104, A2105, A2106, A2107, A2108 G:A361
2qbd A2231 Nb G:A324(N7) A2232, A2233, A2234, A2235, T2236 U:A323, G:A324
2qbd A2187 2Nb G:A858(N7), G:A869(N7) A2188, A2189, A2190, A2191 G:A858, G:A869, C:A868
2qbd A2064 Oph A:A937(OP2) A2065, A2066, A2067, A2068, A2069 A:A938, G:A939
2qbd A2288 Oph G:A100(OP2) A2289, A2290, A2291, A2292, A2293 G:A100, A:A101, G:A64
2qbd A2213 Oph A:A1433(OP2) A2214, A2215, A2216, A2217, A2218 G:A1432 A:A1434, G:A1435
2qbd A2176 Oph G:A21(OP1) A2177, A2178, A2179, A2180, A2181 G:A568, G:A567 A:A573, G:A567
2qbd A2182 Oph·Pout G:A115(OP1) A2183, A2184, A2185, A2186 C:A48
2qbd A2264 Oph·Pout U:A1224(OP1) A2265, A2266, A2267, A2268, A2269 U:A952 C:A1223 A:A977
2qbd A2025 Oph·Pout C:A934(OP1) A2026, A2027, A2028, A2029, A2030 U:A1345
2qbd A2316 Oph·Pout C:A352(OP2) A2317, A2318, A2319, A2320, A2321 G:A354 G:A331, C:A352, C:A330 C:A330, A:A59, G:A354
2qbd A2170 Oph·Pout A:A572(OP1) A2171, A2172, A2173, A2174, A2175 A:A573 A:A819
2qbd A2242 Oph·2Pout A:A608(OP2) A2243, A2244, A2245, A2246, A2247 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608
2qbd A2322 Oph·2Pout G:A111(OP2) A2323, A2324, A2325, A2326, A2327 C:A110, G:A112 G:A112, G:A111
2qbd A2306 Oph·2Pout C:A536(OP1) A2307, A2308, A2309, A2310, A2311 C:A504, G:A537
2qbd A2248 Oph·2Pout A:A1110(OP2) A2249, A2250, A2251, A2252, A2253 A:A1111, C:A1109 U:A1189, A:A1110, A:A1111, C:A1112, A:A1188
2qbd A2001 Oph·3Pout C:A578(OP1) A2002, A2003, A2004, A2005, A2006 C:A576, C:A817, U:A820 G:A575

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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