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 4 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 4qcq A3180 Pout A4178, A4179, E301, E302 A:A864 2qam B3194 Pout B3769, B3770, B3771, B3772, B3773, B3774 G:B649 3v27 A3474 Pout A4528, A4529, A4530, A4531, A4532, A4533 C:A2441 3v23 A3499 Pout A4641, A4642, A4643, A4644 U:A1396 3v27 A3552 Pout A4881, A4882, A4883, A4884, A4885 A:A2459 4qcn A3570 Pout A4912, A4913, A4914, A4915 G:A992 3v23 A3590 Pout A4934, A4935, A4936, A4937, A4938, A4939 U:A464 3v23 A3616 Pout A5088, A5089, A5090, A5091, A5092, A5093 C:A2480 4qcn A3761 Pout A5307, A5308, A5309, A5310, 03105 C:A2275 4dha A3776 Pout A4997, A4998, A4999, A5000, A5001, A5002 G:A2396 4bpp A5028 Pout A7459, A7460, A7461, A7462, A7463, A7464 U:A442 4bpo A5028 Pout A2077, A2078, A2371, A2372, A2373, A2374 U:A442 4bpe A5028 Pout A2079, A2080, A2283, A2356, A2357, A2358 U:A442 4bpn A5028 Pout A6451, A6452, A6453, A6454, A6455, A6456 U:A442 4bpp A5029 Pout A7475, A7476, A7477, A7478, A7479, A7480 A:A437 4bpo A5029 Pout A2074, A2075, A2375, A2376, A2377, A2378 A:A437 4bpe A5029 Pout A2076, A2077, A2284, A2353, A2354, A2355 A:A437 4bpn A5029 Pout A6457, A6458, A6459, A6460, A6461, A6462 A:A437 3td0 B7000 Pout B7001, B7002, B7003, B7004, B7005, B7006 C:B44

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].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>