MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 4ji1 4JI1 (3.14Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of 30s ribosomal subunit from thermus thermophilus List of all 58 Mg2+ binding sites in the PDB structure 4ji1 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 | Next » | 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 4ji1 A1713 Ob G:A610(O6) A2010, A2011, A2012, A2013 A:A608, A:A607 A:A609 4ji1 A1650 Nb G:A324(N7) A1979, A1980, A1981, T301 U:A323, G:A324 4ji1 A1610 Oph A:A766(OP2) A1925, A1926, A1927, A1928 C:A811, A:A767, C:A812 4ji1 A1607 Oph·Pout A:A937(OP2) A1917, A1918, A1919, A1920 A:A938 G:A939, A:A937, A:A938 4ji1 A1633 Oph·Pout A:A1110(OP2) A1957, A1958, A1959 A:A1111 C:A1189, A:A1111 4ji1 A1636 Oph·Pout C:A352(OP2) A1960, A1961, A1962, A1963 G:A354 G:A331, C:A352 C:A330, A:A59, G:A354 4ji1 A1639 Oph·2Pout A:A509(OP2) A1964, A1965, A1966 A:A510, G:A506 4ji1 A1622 Oph·3Pout C:A578(OP1) A1941, A1942, A1943, A1944 U:A820, G:A576, C:A817 4ji1 A1603 trans-2Oph G:A117(OP2), G:A289(OP2) A1903, A1904, A1905, A1906 A:A116, A:A288 G:A117, U:A118 4ji1 A1805 Bout A2521, A2522, A2523, A2524, A2525, A2526 G:A587 4ji1 A1813 2Bout A2567, A2568, A2569, A2570, A2571, A2572 G:A376, G:A377 4ji1 A1735 2Bout A2099, A2100, A2101, A2102, A2103, A2104 C:A699, G:A700 4ji1 A1773 2Bout A2326, A2328, A2329, A2330, A2331, A2332 G:A127, G:A128 4ji1 A1605 2Bout A1907, A1908, A1909, A1910, A1911 G:A1526, G:A1525 4ji1 A1768 2Bout A2296, A2297, A2298, A2299, A2300, A2301 G:A1385, G:A1386 4ji1 A1801 3Bout A2497, A2498, A2499, A2500, A2501, A2502 G:A476, G:A474, G:A475 4ji1 A1727 3Bout A2052, A2053, A2054, A2055, A2056, A2057 A:A101, G:A102, G:A64 4ji1 A1762 2Rout·2Bout A2261, A2262, A2263, A2264, A2265, P201 G:A227, G:A138 C:A137, G:A226 4ji1 A1796 4Bout A2467, A2468, A2469, A2470, A2471, A2472 G:A44, G:A396, U:A45, C:A395 4ji1 A1737 4Bout A2111, A2112, A2113, A2114, A2115, A2116 G:A494, G:A492, G:A490, G:A491

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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