MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbc:B3207, See in JSmolClick on the image to toggle views Site type: 3Pout·Rout·3Bout Schematic drawing for 3Pout·Rout·3Bout List of all 33 Mg2+ binding sites with the site type 3Pout·Rout·3Bout 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 4pec A3129 3Pout·Rout·3Bout A3770, A3771, A3772, A3773, A3774, A3775 G:A570, A:A973, U:A569 A:A972 A:A820, U:A568, A:A821 4qcn A3474 3Pout·Rout·3Bout A4598, A4599, A4600, A4601, A4602, A4603 G:A593, A:A1018, U:A592 G:A1017 A:A867, A:A868, U:A591 4qcp A3385 3Pout·Rout·3Bout A4380, A4381, A4382, A4383, A4384, A4385 G:A570, A:A973, U:A569 G:A972 A:A821, A:A820, U:A568 4too A3017 3Pout·Rout·3Bout A3279, A3280, A3281, A3282, A3283, A3284 A:A1253, A:A582, G:A583 C:A1251 G:A583, C:A584, A:A582 4tp3 A3003 3Pout·Rout·3Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A28, A:A447 A:A447 G:A473, U:A29, G:A30 4tp7 A3018 3Pout·Rout·3Bout A3278, A3279, A3280, A3281, A3282, A3283 A:A582, A:A1253, G:A583 C:A1251 G:A583, C:A584, G:A585 4tpb A3003 3Pout·Rout·3Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A28, A:A447 A:A447 G:A473, U:A29, G:A30 4tpf A3018 3Pout·Rout·3Bout A3279, A3280, A3281, A3282, A3283, A3284 A:A582, A:A1253, G:A583 C:A1251 G:A583, C:A584, A:A582

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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