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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 4bpe




4BPE (3.7Å) -- RIBOSOME : The crystal structure of the eukaryotic 40s ribosomal subunit in complex with eif1 and eif1a - complex 1
List of all 76 Mg2+ binding sites in the PDB structure 4bpe 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
4bpe A5052 Rout A2140, A2141, A2319, A2320, A2321, A2322 A:A675
4bpe A5032 Bout A2150, A2166, A2167, A2168, A2287, A2288 G:A926
4bpe A5068 Bout A2432, A2433, A2452, A2453, A2454, A2474 G:A1562
4bpe A5077 Rout·Bout A2390, A2393, A2394, A2467, A2468, A2469 U:A1277 U:A1277
4bpe A5074 2Bout A2401, A2402, A2403, A2404, A2405, A2463 U:A1385, G:A1389
4bpe A5014 2Bout A2225, A2231, A2232, A2261, A2262, A2263 G:A1617, G:A1707
4bpe A5027 2Bout A2051, A2052, A2053, A2281, A2282, A2360 G:A268, G:A269
4bpe A5016 2Bout A2047, A2048, A2049, A2264, A2265, A2266 G:A194, G:A195
4bpe A5036 2Bout A2097, A2098, A2099, A2299, A2300, A2301 G:A514, U:A515
4bpe A5035 2Bout A2194, A2195, A2196, A2296, A2297, A2298 G:A1028, G:A1029
4bpe A5067 2Bout A2419, A2420, A2421, A2422, A2423, A2451 G:A1478, G:A1479
4bpe A5034 2Bout A2154, A2157, A2159, A2293, A2294, A2295 G:A902, A:A901
4bpe A5013 2Bout A2226, A2227, A2257, A2258, A2259, A2260 G:A1621, U:A1622
4bpe A5045 2Bout A2192, A2193, A2310, A2311, A2312, A2313 C:A1026, U:A1027
4bpe A5011 3Bout A2235, A2236, A2237, A2238, A2255, A2256 G:A1730, G:A1731, U:A1732
4bpe A5040 3Bout A2019, A2026, A2027, A2028, A2304, A2305 U:A57, U:A84, G:A85
4bpe A5000 3Bout A2029, A2030, A2068, A2242, A2243, A2244 U:A94, G:A375, G:A374
4bpe A5044 3Bout A2169, A2170, A2186, A2187, A2308, A2309 G:A958, C:A999, U:A1000
4bpe A5031 3Bout A2151, A2152, A2153, A2158, A2160, A2286 G:A863, G:A903, A:A904
4bpe A5023 3Bout A2018, A2084, A2085, A2086, A2087, A2273 A:A456, G:A457, G:A459

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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