MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3r8s:A2930, See in JSmolClick on the image to toggle views Site type: Oph Schematic drawing for Oph List of all 588 Mg2+ binding sites with the site type Oph in RNA crystal structures in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID" Page 5 of 24 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qbf A1553 Oph C:A1195(OP1) A1655, A1656, A1657, A1658, A1659 A:A1398 2qbf A1564 Oph A:A937(OP2) A1705, A1706, A1707, A1708, A1709 A:A937, A:A938, G:A939 2qbf A1593 Oph G:A100(OP2) A1853, A1854, A1855, A1856, A1857 G:A64, A:A101 2qbg B2922 Oph A:B800(OP1) B3102, B3103, B3104, B3105, B3106 G:B799 A:B191, C:B192 2qbg B2966 Oph U:B419(OP1) B3317, B3318, B3319, B3320, B3321 G:B230 2qbg B2947 Oph A:B1678(OP2) B3224, B3225, B3226, B3227, B3228 A:B1678, A:B1679 2qbh A1578 Oph A:A1433(OP2) A1771, A1772, A1773, A1774, A1775 G:A1432 A:A1434, G:A1435 2qbh A1571 Oph G:A21(OP1) A1741, A1742, A1743, A1744, A1745 A:A573, A:A563, G:A567 2qbh A1554 Oph A:A937(OP2) A1656, A1657, A1658, A1659, A1660 2qbi B2962 Oph A:B800(OP1) B3286, B3287, B3288, B3289, B3290 G:B799, A:B203 C:B192, A:B800 2qbi B2934 Oph U:B419(OP1) B3155, B3156, B3157, B3158, B3159 G:B230 2qbj A1564 Oph A:A937(OP2) A1705, A1706, A1707, A1708, A1709 G:A939, A:A937, A:A938 2qbj A1553 Oph C:A1195(OP1) A1655, A1656, A1657, A1658, A1659 U:A1194 A:A1398 2qbj A1602 Oph C:A980(OP1) A1892, A1893, A1894, A1895, A1896 G:A1221, G:A1220, A:A1219 2qbk B2922 Oph A:B800(OP1) B3101, B3102, B3103, B3104, B3105 G:B799, A:B203 C:B192, A:B800 2qbk B2947 Oph A:B1678(OP2) B3220, B3221, B3222, B3223, B3224 A:B1678, A:B1679 2qbk B2966 Oph U:B419(OP1) B3312, B3313, B3314, B3315, B3316 G:B230 2qou A1570 Oph A:A572(OP1) A2034, A2035, A2036, A2037, A2038 A:A819 2qou A1571 Oph G:A21(OP1) A2039, A2040, A2041, A2042, A2043 G:A567, A:A573, A:A563 2qou A1583 Oph A:A608(OP2) A2093, A2094, A2095, A2096, A2097 C:A631, A:A609, U:A610 2qov B2934 Oph U:B419(OP1) B3156, B3157, B3158, B3159, B3160 C:B418 G:B230 2qov B2962 Oph A:B800(OP1) B3290, B3291, B3292, B3293, B3294 G:B799 A:B191 2qov B2930 Oph A:B945(OP1) B3137, B3138, B3139, B3140, B3141 G:B831 2qow A1562 Oph G:A21(OP1) A1983, A1984, A1985, A1986, A1987 G:A567, G:A568 A:A573, A:A563 2qow A1569 Oph A:A608(OP2) A2014, A2015, A2016, A2017, A2018 A:A630, A:A609, C:A631, U:A610

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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