MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs5:A1545, See in JSmolClick on the image to toggle views Site type: Pout·Bout Schematic drawing for Pout·Bout List of all 223 Mg2+ binding sites with the site type Pout·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 6 of 9 | « 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 3v2d A3266 Pout·Bout A4428, A4429, A4430, A4431, A4432, A4433 G:A1283 G:A1283 3v2f A3513 Pout·Bout A4876, A4877, A4878, A4879, A4880 C:A2283 U:A2390 3v2f A3315 Pout·Bout A4306, A4307, A4308, A4309 A:A1242 G:A1244 3v2f A3508 Pout·Bout A4864, A4865, A4866, A4867, A4868 A:A1809 G:A1807 4a1a 0334 Pout·Bout 07843, 07844, 07845, 07846, 07847, 07848 U:2140 U:2140 4a1e 0345 Pout·Bout 08115, 08116, 08117, 08118, 08119, 08120 A:289 G:290 4bpe A5072 Pout·Bout A2414, A2415, A2417, A2418, A2458, A2459 U:A1467 U:A1492 4bpe A5061 Pout·Bout A2364, A2365, A2366, A2441, A2442, A2443 A:A613 A:A1008 4bpe A5076 Pout·Bout A2427, A2428, A2430, A2431, A2465, A2466 G:A1533 G:A1531 4bpe A5006 Pout·Bout A2216, A2217, A2218, A2248, A2249, A2250 G:A1271 G:A1269 4bpe A5065 Pout·Bout A2416, A2435, A2436, A2437, A2447, A2448 C:A1466 C:A1568 4bpn A5006 Pout·Bout A6060, A6067, A6074, A6081, A6088, A6095 G:A1271 G:A1269 4bpn A5061 Pout·Bout A6235, A6236, A6237, A6238, A6239, A6241 A:A613 A:A1008 4bpn A5065 Pout·Bout A6521, A6522, A6523, A6524, A6525, A6526 C:A1466 C:A1568 4bpn A5071 Pout·Bout A6563, A6564, A6565, A6566, A6567, A6569 C:A1418 C:A1185 4bpn A5076 Pout·Bout A6599, A6600, A6601, A6602, A6603, A6604 G:A1533 G:A1531 4bpo A5072 Pout·Bout A2274, A2275, A2276, A2278, A2457, A2458 U:A1467 U:A1492 4bpo A5006 Pout·Bout A2244, A2245, A2246, A2329, A2330, A2331 G:A1271 G:A1269 4bpo A5061 Pout·Bout A2137, A2138, A2139, A2436, A2437, A2438 A:A613 A:A1008 4bpo A5076 Pout·Bout A2288, A2289, A2290, A2291, A2464, A2465 G:A1533 G:A1531 4bpo A5065 Pout·Bout A2277, A2295, A2296, A2297, A2442, A2443 C:A1466 C:A1568 4bpp A5078 Pout·Bout A8259, A8260, A8261, A8262, A8263, A8264 U:A1277 G:A1296 4bpp A5065 Pout·Bout A8051, A8052, A8053, A8054, A8055, A8056 C:A1466 C:A1568 4bpp A5061 Pout·Bout A7987, A7988, A7989, A7990, A7991, A7992 A:A613 A:A1008 4bpp A5076 Pout·Bout A8227, A8228, A8229, A8230, A8231, A8232 G:A1533 G:A1531

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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