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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"
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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
2qbd A2038 Oph·4Pout A:A560(OP2) A2039, A2040, A2041, A2042, A2043 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
2qbd A2226 Oph·Ob G:A558(OP1) G:A299(O6) A2227, A2228, A2229, A2230 A:A560 G:A297 G:A566, A:A298
2qbd A2237 Oph·Ob A:A533(OP1) U:A516(O4) A2238, A2239, A2240, A2241 A:A532 G:A515, G:A517
2qbd A2259 Oph·Ob U:A1095(OP2) G:A1108(O6) A2260, A2261, A2262, A2263 G:A1068
2qbd A2301 Oph·Ob A:A195(OP2) U:A180(O4) A2302, A2303, A2304, A2305 C:A194, A:A179 A:A181, A:A179
2qbd A2055 cis-2Oph C:A1054(OP2), A:A1197(OP2) A2056, A2057, A2058, A2059 G:A1198 G:A1053 G:A1198, U:A1199, A:A1197
2qbd A2091 cis-2Oph A:A509(OP2), A:A510(OP2) A2092, A2093, A2094, A2095 G:A506, C:A507 U:A508 A:A510
2qbd A2205 cis-2Oph A:A964(OP1), U:A1199(OP1) A2206, A2207, A2208, A2209 U:A965, G:A1198
2qbd A2254 cis-2Oph G:A1068(OP1), G:A1094(OP1) A2255, A2256, A2257, A2258 G:A1387, C:A1388
2qbd A2210 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) A2211, A2212 U:A982 G:A1221, U:A982
2qbd A2060 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A2061, A2062, A2063 A:A1196
2qbd A2284 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A2285, A2286, A2287 G:A1504, U:A1498 A:A1500
2qbd A2021 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A2022, A2023, A2024 U:A571
2qbd A2051 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A2052, A2053, A2054 C:A1501, G:A1504 U:A1506
2qbd A2312 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2313, A2314, A2315 A:A288 G:A117, U:A118
2qbd A2294 Bout A2295, A2296, A2297, A2298, A2299, A2300 G:A38
2qbd A2270 2Bout A2271, A2272, A2273, A2274, A2275, A2276 G:A1525, G:A1526
2qbd A2157 2Bout A2158, A2159, A2160, A2161, A2162, A2163 G:A941, G:A942
2qbd A2192 2Bout A2193, A2194, A2195, A2196, A2197, A2198 G:A1385, G:A1386
2qbd A2349 3Bout A2350, A2351, A2352, A2353, A2354 C:A1359, G:A976, U:A1358

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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