MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3i1q:A1540, See in JSmolClick on the image to toggle views Site type: 4Pout·Rout·Bout Schematic drawing for 4Pout·Rout·Bout List of all 10 Mg2+ binding sites with the site type 4Pout·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 1 of 1

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qox B2938 4Pout·Rout·Bout B3180, B3181, B3182, B3183, B3184 G:B2446, G:B2447, G:B2502, C:B2501 U:B576 G:B2502 3i1q A1540 4Pout·Rout·Bout A1605, A1606, A1607, A1608, A1609 G:A557, A:A560, U:A562, G:A558 A:A559 A:A300 3ofd A2965 4Pout·Rout·Bout A3328, A3329, A3330, A3331, A3332 U:A2026, U:A2034, C:A2025, A:A2033 A:A2033 U:A2026 3ofq A2984 4Pout·Rout·Bout A3420, A3421, A3422, A3423, C477 A:A2587, G:A2588, A:A2589, A:A2600 A:A2439 A:A2589 3v2f A3434 4Pout·Rout·Bout A4652, A4653, A4654, A4655, A4656 A:A933, U:A839, C:A838, G:A818 G:A932 G:A932 4dr6 A1633 4Pout·Rout·Bout A2085, A2086, A2087, A2088 G:A557, U:A560, C:A562, G:A558 A:A559 G:A566 4dv1 A1811 4Pout·Rout·Bout A2212, A2213, A2214, A2215, A2216 U:A114, C:A307, G:A115, C:A47 G:A306 G:A31 4tp3 A3073 4Pout·Rout·Bout A3532, A3533, A3534, A3535, A3536 A:A2518, U:A2519, A:A2541, C:A2540 C:A2517 A:A2541 4tpb A3073 4Pout·Rout·Bout A3532, A3533, A3534, A3535, A3536 A:A2518, U:A2519, A:A2541, C:A2540 C:A2517 A:A2541 4tpf A3045 4Pout·Rout·Bout A3393, A3394, A3395, A3396, A3397, A3398 U:A1352, G:A1377, C:A1376, C:A1351 C:A1376 G:A1377

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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