MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2avy:A1578, See in JSmolClick on the image to toggle views Site type: Pout·Rout Schematic drawing for Pout·Rout List of all 37 Mg2+ binding sites with the site type Pout·Rout 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 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 1dno B23 Pout·Rout B209, B210, B211, B212, B213, B214 DC:B20 DC:B20 1jj2 A8065 Pout·Rout 03497, 09450, A8523, A8552, A8603, A8633 C:0783 G:0782 1k73 C8065 Pout·Rout A3966, A9924, C8521, C8551, C8603, C8634 C:A783 G:A782 1k9m C8065 Pout·Rout A3961, A9912, C8522, C8552, C8604, C8633 C:A783 G:A782 1m90 C8065 Pout·Rout A3496, A9444, C8525, C8551, C8598, C8626 C:A783 G:A782 1nji C8065 Pout·Rout A3960, A9920, C8523, C8549, C8601, C8631 C:A783 G:A782 1s72 A8065 Pout·Rout 03492, 09447, A8523, A8552, A8604, A8634 C:0783 G:0782 1vq5 A8065 Pout·Rout 03248, 04282, A9320, A9344, A9395, A9424 C:0783 G:0782 1vq7 A8065 Pout·Rout 03248, 04294, A9320, A9350, A9397, A9426 C:0783 G:0782 1yij A8065 Pout·Rout 03980, 09933, A8820, A8846, A8898, A8927 C:0783 G:0782 2avy A1578 Pout·Rout A1772, A1773, A1774, A1775, A1776, A1777 U:A916 U:A13 2otl A8065 Pout·Rout 03981, 09933, A8718, A8750, A8796, A8826 C:0783 G:0782 3cc2 A8065 Pout·Rout 03524, 09468, A8521, A8547, A8594, A8624 C:0783 G:0782 3cc7 A8050 Pout·Rout 04012, 09962, A8987, A9013, A9055, A9087 C:0783 G:0782 3i1p A2918 Pout·Rout A3112, A3113, A3114, A3115, A3116, A3117 G:A1256 U:A1255 3i1s A1570 Pout·Rout A1761, A1762, A1763, A1764, A1765 C:A503 C:A522 3i1t A2918 Pout·Rout A3111, A3112, A3113, A3114, A3115, A3116 G:A1256 U:A1255 3v27 A3619 Pout·Rout A5171, A5172, A5173, A5174, A5175, A5176 G:A680 G:A189 3v28 A1754 Pout·Rout A2031, A2032, A2033, L201, L202 G:A537 C:A503 3v2c A1642 Pout·Rout A1934, A1935, A1936, A1937 C:A934 U:A1345 4a1a 08 Pout·Rout 05059, 05060, 05061, 05062, 05063, 05064 C:238 G:236 4bpe A5007 Pout·Rout A2001, A2128, A2129, A2251, A2345, A2346 A:A600 C:A4 4bpn A5052 Pout·Rout A6173, A6174, A6175, A6176, A6177, A6178 C:A672 A:A675 4bpn A5007 Pout·Rout A6102, A6109, A6116, A6123, A6130, A6137 A:A600 C:A4 4bpo A5007 Pout·Rout A2001, A2128, A2129, A2332, A2333, A2334 A:A600 C:A4

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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