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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 4bpo




4BPO (3.7Å) -- RIBOSOME : The crystal structure of the eukaryotic 40s ribosomal subunit in complex with eif1 and eif1a - complex 3
List of all 77 Mg2+ binding sites in the PDB structure 4bpo 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
4bpo A5068 Bout A2292, A2293, A2448, A2449, A2450, A2451 G:A1562
4bpo A5016 Bout A2048, A2049, A2349, A2350, A2351, A2352 G:A194
4bpo A5077 Rout·Bout A2250, A2252, A2253, A2299, A2300, A2466 U:A1277 U:A1277
4bpo A5036 2Bout A2095, A2096, A2097, A2395, A2396, A2397 G:A514, U:A515
4bpo A5014 2Bout A2303, A2309, A2310, A2346, A2347, A2348 G:A1617, G:A1707
4bpo A5013 2Bout A2304, A2305, A2342, A2343, A2344, A2345 G:A1621, U:A1622
4bpo A5027 2Bout A2051, A2052, A2367, A2368, A2369, A2370 G:A268, G:A269
4bpo A5067 2Bout A2279, A2280, A2281, A2282, A2283, A2447 G:A1478, G:A1479
4bpo A5032 2Bout A2156, A2170, A2171, A2172, A2382, A2383 G:A926, U:A925
4bpo A5035 2Bout A2198, A2199, A2200, A2392, A2393, A2394 G:A1028, G:A1029
4bpo A5045 2Bout A2196, A2197, A2406, A2407, A2408, A2409 C:A1026, U:A1027
4bpo A5034 2Bout A2159, A2161, A2162, A2164, A2390, A2391 G:A902, A:A901
4bpo A5024 3Bout A2241, A2242, A2243, A2248, A2362, A2363 G:A1266, G:A1267, A:A1268
4bpo A5011 3Bout A2313, A2314, A2315, A2316, A2339, A2340 G:A1730, G:A1731, U:A1732
4bpo A5031 3Bout A2157, A2158, A2163, A2165, A2380, A2381 G:A863, G:A903, A:A904
4bpo A5000 3Bout A2030, A2031, A2066, A2320, A2321, A2322 U:A94, G:A375, G:A374
4bpo A5023 3Bout A2018, A2082, A2083, A2084, A2085, A2361 A:A456, G:A457, G:A459
4bpo A5074 3Bout A2261, A2262, A2263, A2264, A2265, A2462 U:A1385, A:A1388, G:A1389
4bpo A5040 3Bout A2019, A2026, A2027, A2028, A2029, A2400 U:A57, U:A84, G:A85
4bpo A5044 3Bout A2173, A2174, A2190, A2191, A2404, A2405 G:A958, C:A999, U:A1000

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].


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