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 4nvu 4NVU (3Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of antibiotic dityromycin bound to 70s ribosome List of all 9 Mg2+ binding sites in the PDB structure 4nvu 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 4nvu A3187 Ob G:A1432(O6) A4092, A4093, A4094, A4095 C:A1466 G:A1467 4nvu A3175 Oph C:A352(OP2) A4066, A4067, A4068, A4069 C:A352 C:A330, A:A59, G:A354 4nvu A3182 Oph G:A21(OP1) A4080, A4081, A4082, A4083, A4084 G:A568, G:A567 G:A567, A:A573 4nvu A3152 Oph A:A766(OP2) A4025, A4026, A4027, A4028 C:A811, C:A812, U:A813, A:A767 4nvu A3155 3Bout A4032, A4033, A4034, A4035 G:A44, U:A45, G:A396 4nvu A3165 Pout·2Bout A4048, A4049, A4050, A4051 G:A803 G:A771, U:A772 4nvu A3145 Pout·3Bout A4012, A4013, O101, O102 A:A583 G:A584, G:A585, U:A757 4nvu A3205 2Pout A4129, A4130, E202, E203 A:A864, U:A863 4nvu A3192 4Pout A4104, A4105, A4106, A4107, A4108, A4109 U:A13, U:A14, G:A15, A:A16

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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