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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 2qow



2QOW (3.93Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin. this file contains the 30s subunit of the second 70s ribosome, with spectinomycin bound. the entire crystal structure contains two 70s ribosomes.
List of all 54 Mg2+ binding sites in the PDB structure 2qow 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
2qow A1587 3Pout A2100, A2101, A2102, A2103, N266, N1813 G:A1048, U:A1049, A:A1204
2qow A1588 Pout·2Bout A2104, A2105, A2106, A2107, A2108, A2109 A:A1046 G:A1047, G:A1048
2qow A1589 Pout·3Bout A2110, A2111, N280, N281, N1823, N1826 A:A1360 C:A980, G:A1361, A:A1360
2qow A1590 2Bout A2112, A2113, A2114, A2115, A2116 G:A1050, G:A1207
2qow A1591 2Pout·Rout·Bout A2120, A2121, A2122, A2123, A2124, A2125 G:A1356, A:A1357 A:A1254 C:A1359
2qow A1592 2Bout A2126, A2127, A2128, A2129, A2130, A2131 G:A941, G:A942
2qow A1593 Pout·2Bout A2132, A2133, A2134, A2135, A2136, A2137 G:A1385 G:A1385, G:A1386
2qow A1594 Ob G:A1370(O6) A2138, A2139, A2140, A2141, A2142 U:A1372, U:A1351, G:A1371
2qow A1595 Oph·2Pout U:A1199(OP1) A2143, A2144, A2145, A2146 A:A964, G:A1198
2qow A1596 Oph·2Ob C:A980(OP2) U:A981(O4), G:A1222(O6) A2147, A2148 U:A982 G:A1221, U:A982
2qow A1597 Oph·2Pout A:A1110(OP2) A2149, A2150, A2151, A2152, A2153 A:A1111, C:A1109 U:A1189, A:A1110, A:A1111
2qow A1598 cis-2Oph G:A1068(OP1), G:A1094(OP1) A2154, A2155, A2156, A2157 C:A1388
2qow A1599 Oph·Ob U:A1095(OP2) G:A1108(O6) A2158, A2159, A2160, A2161 C:A1096 G:A1094 C:A1109
2qow A1600 Oph·Pout U:A1224(OP1) A2162, A2163, A2164, A2165, A2166 U:A952 C:A1223 A:A977

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>