MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 1nuv 1NUV (1.81Å) -- RNA : The leadzyme ribozyme bound to mg(h2o)6(ii) and sr(ii) at 1.8 a resolution List of all 8 Mg2+ binding sites in the PDB structure 1nuv in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "Site type" 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 1nuv G414 3Bout G202, G203, G205, G206, H201, H204 A:G29, G:G30, G:H39 1nuv A410 3Bout A412, A413, A414, A415, A416, B425 G:A20, G:A19, U:B47 1nuv A411 3Bout A417, A418, A419, A420, B426, B427 A:A29, G:A30, G:B39 1nuv E417 3Bout E285, E287, E302, E367, E370, F293 A:E29, G:E30, G:F39 1nuv G413 3Bout G222, G224, G225, H221, H223, H226 G:G20, G:G19, U:H47 1nuv E416 3Bout E90, E93, E112, E117, E305, F294 G:E19, G:E20, U:F47 1nuv B412 2Pout·3Bout A421, A422, A423, B428, B429, B430 G:A26, A:A25 U:B41, G:B42, G:B43 1nuv H415 2Pout·3Bout G228, G229, G231, H227, H230, H232 G:G26, A:G25 U:H41, G:H42, G:H43

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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