MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1egk:C14, See in JSmolClick on the image to toggle views Site type: Bout Schematic drawing for Bout List of all 132 Mg2+ binding sites with the site type Bout 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 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v28 A1725 Bout A1931, A1932, A1933, A1934 G:A771 3v2d A3689 Bout A5642, A5643, A5644, A5645, A5646, A5647 G:A2000 3v2d A3718 Bout A5747, A5748, A5749, A5750 G:A993 4a17 0334 Bout 08499, 08500, 08501, 08502, 08503, 08504 G:2141 4a17 071 Bout 05715, 05716, 05717, 05718, 05719, 05720 U:210 4a1e 0117 Bout 05987, 05988, 05989, 05990, 05991, 05992 G:382 4a1e 0334 Bout 08003, 08004, 08005, 08006, 08007, 08008 G:2141 4bpe A5032 Bout A2150, A2166, A2167, A2168, A2287, A2288 G:A926 4bpe A5068 Bout A2432, A2433, A2452, A2453, A2454, A2474 G:A1562 4bpn A5068 Bout A6542, A6543, A6544, A6545, A6546, A6548 G:A1562 4bpn A5059 Bout A6222, A6223, A6224, A6225, A6226, A6227 C:A1691 4bpn A5055 Bout A6193, A6194, A6195, A6196, A6198, A6199 C:A1736 4bpn A5032 Bout A6033, A6034, A6035, A6036, A6037, A6038 G:A926 4bpo A5016 Bout A2048, A2049, A2349, A2350, A2351, A2352 G:A194 4bpo A5068 Bout A2292, A2293, A2448, A2449, A2450, A2451 G:A1562 4bpp A5032 Bout A7523, A7524, A7525, A7526, A7527, A7528 G:A926 4dha A3620 Bout A4443, A4444, A4445, A4446, A4447, A4448 G:A2000 4dhb A1815 Bout A2194, A2195, A2196, A2197, A2198 G:A587 4dhc A3459 Bout A4061, A4062, A4063, A4064 G:A83 4dhc A3673 Bout A4655, A4656, A4657, A4658, A4659, A4660 G:A1388 4dr2 A1668 Bout A2147, A2148, A2149, A2150 G:A577 4dr2 A1776 Bout A2472, A2473, A2474, A2475 U:A871 4dr2 A1675 Bout A2162, A2163, A2164, A2165, A2166 G:A587 4dr2 A1753 Bout A2396, A2397, A2398, A2399 G:A700 4dr2 A1711 Bout A2259, A2260, A2261, A2262 G:A226

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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