MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs6:B2935, See in JSmolClick on the image to toggle views Site type: 4Pout·2Bout Schematic drawing for 4Pout·2Bout List of all 40 Mg2+ binding sites with the site type 4Pout·2Bout 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 A1862 4Pout·2Bout A2736, A2737, A2738, A2739, A2740, A2741 U:A757, G:A581, G:A758, U:A580 G:A758, G:A581 4dv5 A1842 4Pout·2Bout A2212, A2213, A2214, A2215, A2216, A2217 U:A757, G:A758, U:A580, G:A581 G:A758, G:A581 4ji5 A1725 4Pout·2Bout A2066, A2067, A2068, A2069, A2070, A2071 U:A580, G:A758, U:A757, G:A581 G:A581, G:A758 4pec A3061 4Pout·2Bout A3476, A3477, A3478, A3479, A3480, A3481 C:A2050, A:A2614, A:A2051, G:A2578 A:A2051, A:A2614 4pec A3056 4Pout·2Bout A3452, A3453, A3454, A3455, A3456, A3457 G:A1959, A:A1937, C:A1958, A:A1936 G:A1959, A:A1960 4qcn A3557 4Pout·2Bout A4868, A4869, A4870, A4871, A4872 G:A1680, G:A1676, A:A1679, U:A1675 G:A1676, C:A1677 4qcp A3551 4Pout·2Bout A4762, A4763, A4764, A4765, A4766, A4767 A:A1936, C:A1958, G:A1959, A:A1937 A:A1960, G:A1959 4qcr A3580 4Pout·2Bout A4889, A4890, A4891, A4892, A4893 G:A1680, G:A1676, A:A1679, U:A1675 G:A1676, C:A1677 4qct A3570 4Pout·2Bout A4793, A4794, A4795, A4796, A4797, A4798 A:A1936, C:A1958, G:A1959, A:A1937 A:A1960, G:A1959 4qd1 A3558 4Pout·2Bout A4613, A4614, A4615, A4616, A4617, A4618 A:A1936, C:A1958, G:A1959, A:A1937 G:A1959, A:A1960 4tov A3063 4Pout·2Bout A3481, A3482, A3483, A3484, A3485, A3486 G:A2578, U:A2613, A:A2614, A:A2051 A:A2051, A:A2614 4tox A3063 4Pout·2Bout A3479, A3480, A3481, A3482, A3483, A3484 C:A2050, A:A2614, A:A2051, G:A2578 A:A2051, A:A2614 4tp3 A3062 4Pout·2Bout A3478, A3479, A3480, A3481, A3482, A3483 A:A2614, A:A2051, G:A2578, C:A2050 A:A2051, A:A2614 4tp9 A3063 4Pout·2Bout A3481, A3482, A3483, A3484, A3485, A3486 U:A2613, A:A2614, A:A2051, G:A2578 A:A2051, A:A2614 4tpb A3062 4Pout·2Bout A3478, A3479, A3480, A3481, A3482, A3483 A:A2614, A:A2051, G:A2578, C:A2050 A:A2051, A:A2614

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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