MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 4ji1:A1760, See in JSmolClick on the image to toggle views Site type: 3Pout·2Rout Schematic drawing for 3Pout·2Rout List of all 11 Mg2+ binding sites with the site type 3Pout·2Rout 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 1 of 1

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3oxb A111 3Pout·2Rout A149, A150, A151, A152, A153 A:A21, U:A20, C:A15 A:A13, C:B24 4ji5 A1697 3Pout·2Rout A1911, A1912, A1913, A1914, A1915, A1916 G:A1215, C:A984, G:A1050 C:A1214, G:A1048 4ji1 A1760 3Pout·2Rout A2249, A2250, A2251, A2252, A2253, A2254 C:A1051, U:A1052, C:A1200 C:A962, G:A963 4duy A1789 3Pout·2Rout A2126, A2127, A2128, A2129, A2130, A2131 C:A1200, C:A1051, U:A1052 C:A962, G:A963 4ji7 A1824 3Pout·2Rout A2458, A2459, A2460, A2461, A2462, A2463 C:A984, G:A1050, G:A1215 C:A1214, G:A1050 3i22 A2978 3Pout·2Rout A3394, A3395, A3396, A3397, A3398 G:A2447, G:A2502, C:A2501 A:A575, U:A576 3v2d A3149 3Pout·2Rout A4099, A4100, A4101, A4102, A4103 G:A690, A:A781, A:A782 U:A1777, G:A780 4bpp A5003 3Pout·2Rout A7059, A7060, A7061, A7062, A7063, A7064 G:A1013, A:A1014, G:A844 A:A843, U:A842 4bpn A5003 3Pout·2Rout A6018, A6019, A6020, A6021, A6022, A6023 G:A1013, A:A1014, G:A844 A:A843, U:A842 4bpe A5003 3Pout·2Rout A2144, A2145, A2146, A2147, A2189, A2352 A:A1014, G:A844, G:A1013 U:A842, A:A843 4bpo A5064 3Pout·2Rout A2226, A2227, A2228, A2234, A2269, A2270 A:A1180, U:A1420, G:A1419 U:A1241, G:A1240

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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