MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbd:A2143, See in JSmolClick on the image to toggle views Site type: 2Pout·Rout Schematic drawing for 2Pout·Rout List of all 39 Mg2+ binding sites with the site type 2Pout·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 1vt2 A2964 2Pout·Rout A3323, A3324, A3325, A3326 G:A2592, G:A1973 C:A1967 2qbd A2143 2Pout·Rout A2144, A2145, A2146, A2147, A2148, A2149 A:A1357, G:A1356 A:A1254 3df3 A2324 2Pout·Rout A4325, A4326, A4327, A4328, A4329 C:A504, C:A536 C:A522 3i1p A2964 2Pout·Rout A3320, A3321, A3322, A3323 G:A2592, G:A1973 C:A1967 3i1t A2964 2Pout·Rout A3323, A3324, A3325, A3326 G:A1973, G:A2592 C:A1967 3i22 A2918 2Pout·Rout A3109, A3110, A3111, A3112, A3113, A3114 U:A2016, G:A1256 U:A1255 3i22 A2972 2Pout·Rout A3367, A3368, A3369, C476, C479 G:A2239, U:A2240 G:A2238 3i22 A2963 2Pout·Rout A3322, A3323, A3324, A3325 G:A2592, G:A1973 C:A1967 3oas A2963 2Pout·Rout A3321, A3322, A3323, A3324 G:A2592, G:A1973 C:A1967 3ofc A2949 2Pout·Rout A3251, A3252, A3253, A3254, A3255 G:A1455, A:A1453 C:A1454 3og0 A2962 2Pout·Rout A3319, A3320, A3321, A3322 G:A2592, G:A1973 C:A1967 3ora A1573 2Pout·Rout A1765, A1766, A1767, A1768, A1769 C:A536, A:A523 C:A522 3v27 A3372 2Pout·Rout A4116, A4117, A4118, A4119, A4120 G:A1989, C:A1990 G:A1667 3v27 A3484 2Pout·Rout A4570, A4571, A4572, A4573, A4574, A4575 A:A324, G:A323 A:A324 3v27 A3545 2Pout·Rout A4849, A4850, A4851, A4852, A4853 G:A1555, C:A698 A:A1554 3v27 A3424 2Pout·Rout A4321, A4322, A4323, 1201, 1202 U:A2233, U:A380 G:A379 3v29 A3455 2Pout·Rout A4238, A4239, A4240, A4241 C:A365, C:A404 U:A403 3v29 A3594 2Pout·Rout A4757, A4758, A4759, A4760, A4761, A4762 A:A529, G:A530 A:A528 3v29 A3448 2Pout·Rout A4211, A4212, B307, B308, B309, B310 A:B102, G:B72 C:A915 3v2d A3720 2Pout·Rout A5753, A5754, A5755, A5756 U:A1540, C:A1543 A:A1542 4a1e 08 2Pout·Rout 05075, 05076, 05077, 05078, 05079, 05080 C:238, A:237 G:236 4dr5 A1836 2Pout·Rout A2402, A2403, A2404, A2405, A2406, A2407 G:A450, A:A452 A:A451 4duy A1859 2Pout·Rout A2395, A2396, A2397, A2398, A2399, A2400 C:A972, C:A1366 G:A971 4duy A1838 2Pout·Rout A2318, A2319, M204, M205, M206, M207 C:A1322, A:A1225 G:A1224 4duy A1818 2Pout·Rout A2241, A2242, A2243, A2244, A2245 C:A1103, A:A1101 C:A1100

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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