MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs6:B2970, See in JSmolClick on the image to toggle views Site type: 3Pout·Rout·Bout Schematic drawing for 3Pout·Rout·Bout List of all 36 Mg2+ binding sites with the site type 3Pout·Rout·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 2 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 4dr7 A1631 3Pout·Rout·Bout A2081, A2082, A2083, A2084 U:A560, C:A562, G:A558 A:A559 G:A566 4duz A1842 3Pout·Rout·Bout A2228, A2229, A2230, A2231, A2232 G:A951, G:A1224, U:A952 C:A1223 A:A977 4dv1 A1793 3Pout·Rout·Bout A2120, A2121, A2122, A2123, A2124, A2125 C:A150, A:A151, G:A168 G:A167 G:A168 4dv3 A1818 3Pout·Rout·Bout A2115, A2116, A2117, A2118, A2119, A2120 C:A150, A:A151, G:A168 G:A167 G:A168 4dv5 A1812 3Pout·Rout·Bout A2109, A2110, A2111, A2112, A2113, A2114 A:A151, G:A168, C:A150 G:A167 G:A168 4gar A3065 3Pout·Rout·Bout A3508, A3509, A3510, A3511 C:A2066, G:A2067, C:A2248 A:A2247 U:A2249 4gar A3019 3Pout·Rout·Bout A3299, A3300, A3301, A3302 G:A760, A:A761, G:A733 C:A732 G:A733 4ji6 A1873 3Pout·Rout·Bout A2852, A2853, A2854, A2855, A2856, A2857 C:A536, C:A504, G:A505 A:A535 G:A505 4pec A3047 3Pout·Rout·Bout A3407, A3408, A3409, A3410, A3411 G:A1455, G:A1456, A:A1453 C:A1454 U:A1457 4qcn A3457 3Pout·Rout·Bout A4542, A4543, A4544, A4545, A4546 A:A1655, C:A1663, G:A1665 C:A1663 G:A1665 4tp7 A3064 3Pout·Rout·Bout A3482, A3483, A3484, A3485 G:A2505, G:A2056, G:A2057 A:A2503 A:A2058

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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