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 4ji8 4JI8 (3.74Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of 30s ribosomal subunit from thermus thermophilus List of all 29 Mg2+ binding sites in the PDB structure 4ji8 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4ji8 A1684 Ob G:A1370(O6) A2143, A2144, A2145 U:A1372 4ji8 A1761 Ob G:A610(O6) A2174, A2175, A2176, A2177 A:A608 A:A609 4ji8 A1670 Nb G:A324(N7) A2121, A2122, A2123, T201 4ji8 A1649 Oph C:A352(OP2) A2092, A2093, A2094, A2095 G:A331, C:A352 A:A59, G:A354 4ji8 A1611 Oph·Pout A:A937(OP2) A2027, A2028, A2029, A2030 A:A938 G:A939, A:A937, A:A938 4ji8 A1652 Oph·2Pout A:A509(OP2) A2097, A2098, A2099 A:A510, G:A506 C:A508 4ji8 A1632 Oph·3Pout C:A578(OP1) A2064, A2065, A2066, A2067 U:A820, G:A576, C:A817 4ji8 A1619 Oph·Nb A:A766(OP2) C:A812(N3) A2042, A2043, A2044, A2045 U:A813, C:A811 4ji8 A1604 trans-2Oph G:A117(OP2), G:A289(OP2) A2004, A2005, A2006, A2007 A:A116, A:A288 G:A115 G:A117 4ji8 A1950 4Bout A3205, A3206, A3207, A3208, A3209, A3210 C:A43, G:A44, U:A45, G:A396 4ji8 A1680 4Bout A2138, N201, N202, N203 A:A1360, G:A1361, C:A980, C:A979 4ji8 A1893 Pout·Bout A2870, A2871, A2872, A2873, A2874, A2875 G:A129 C:A131 4ji8 A1638 Pout·Bout A2073, A2074, A2075, A2076 C:A754 G:A587 4ji8 A1963 Pout·Rout·Bout A3282, A3283, A3284, A3285, A3286, A3287 G:A799 C:A699 G:A698 4ji8 A1977 Pout·3Bout A3348, A3349, A3350, A3351, A3352, A3353 A:A781 G:A798, G:A799, G:A800 4ji8 A1781 Pout·3Bout A2212, A2213, A2214, A2215, A2216, A2217 U:A871 U:A833, G:A853, G:A854 4ji8 A1872 Pout·4Bout A2754, A2755, A2756, A2757, A2758, A2759 G:A1057 C:A1059, G:A1198, U:A1199, G:A1058 4ji8 A1609 2Pout·Bout A2019, A2020, A2021, A2022, A2023 C:A620, A:A621 G:A617 4ji8 A1832 2Pout·3Bout A2514, A2515, A2516, A2517, A2518, A2519 U:A804, G:A803 G:A771, U:A772, C:A770 4ji8 A1866 2Pout·5Bout A2718, A2719, A2720, A2721, A2722, A2723 A:A414, A:A415 G:A426, U:A427, G:A428, G:A416, C:A417

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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