MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4m:A1592, See in JSmolClick on the image to toggle views Site type: Pout Schematic drawing for Pout List of all 94 Mg2+ binding sites with the site type Pout 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 3 of 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4a1a 0199 Pout 06611, 06612, 06613, 06614, 06615, 06616 A:381 4a1c 054 Pout 05251, 05252, 05253, 05254, 05255, 05256 U:258 4a1e 070 Pout 05635, 05636, 05637, 05638, 05639, 05640 A:25 4a1e 0199 Pout 06755, 06756, 06757, 06758, 06759, 06760 A:381 4a1e 0366 Pout 08355, 08356, 08357, 08358, 08359, 08360 G:234 4a1e 054 Pout 05459, 05460, 05461, 05462, 05463, 05464 U:258 4a1e 079 Pout 05715, 05716, 05717, 05718, 05719, 05720 A:24 4a1e 055 Pout 05475, 05476, 05477, 05478, 05479, 05480 G:259 4a1e 06 Pout 05059, 05060, 05061, 05062, 05063, 05064 U:2140 4bpe A5029 Pout A2076, A2077, A2284, A2353, A2354, A2355 A:A437 4bpe A5028 Pout A2079, A2080, A2283, A2356, A2357, A2358 U:A442 4bpn A5029 Pout A6457, A6458, A6459, A6460, A6461, A6462 A:A437 4bpn A5028 Pout A6451, A6452, A6453, A6454, A6455, A6456 U:A442 4bpo A5028 Pout A2077, A2078, A2371, A2372, A2373, A2374 U:A442 4bpo A5029 Pout A2074, A2075, A2375, A2376, A2377, A2378 A:A437 4bpp A5029 Pout A7475, A7476, A7477, A7478, A7479, A7480 A:A437 4bpp A5028 Pout A7459, A7460, A7461, A7462, A7463, A7464 U:A442 4dha A3776 Pout A4997, A4998, A4999, A5000, A5001, A5002 G:A2396 4dr2 A1727 Pout A2303, A2304, A2305, A2306 G:A475 4dr2 A1689 Pout A2199, A2200, A2201, A2202 G:A1079 4dr2 A1733 Pout A2320, A2321, A2322, A2323 A:A448 4dr2 A1775 Pout A2468, A2469, A2470, A2471 C:A882 4dr2 A1725 Pout A2295, A2296, A2297, A2298 G:A371 4dr4 A1728 Pout A2240, A2241, A2242, A2243 G:A371 4dr4 A1648 Pout A2070, A2071, A2072, A2073 U:A20

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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