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 4nw0 4NW0 (3.1Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of antibiotic ge82832 bound to 70s ribosome List of all 6 Mg2+ binding sites in the PDB structure 4nw0 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 4nw0 A3132 Oph·Pout C:A770(OP1) A4114, A4115, A4116, A4117 C:A1514 4nw0 A3103 2Bout A4067, A4068, A4069, A4070, A4071 G:A895, G:A894 4nw0 A3102 Pout·Rout·3Bout A4063, A4064, A4065, A4066 G:A21 G:A567 G:A567, A:A573, A:A563 4nw0 A3090 2Pout·Bout A4038, A4039, A4040, A4041 U:A804, G:A803 G:A771 4nw0 A3152 3Pout·2Bout A4153, A4154, A4155, A4156 U:A580, G:A581, G:A758 G:A581, G:A758 4nw0 A3083 4Pout·Bout A4021, A4022, A4023, A4024 A:A768, U:A804, C:A805, A:A767 A:A768

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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