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 4a1a 4A1A (3.52Å) -- RIBOSOME : T.thermophila 60s ribosomal subunit in complex with initiation factor 6. this file contains 5s rrna, 5.8s rrna and proteins of molecule 3. List of all 15 Mg2+ binding sites in the PDB structure 4a1a 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 4a1a 0324 2Bout 07699, 07700, 07701, 07702, 07703, 07704 G:318, A:317 4a1a 066 3Bout 05507, 05508, 05509, 05510, 05511, 05512 G:216, U:217, G:215 4a1a 0117 3Bout 05859, 05860, 05861, 05862, 05863, 05864 G:382, G:383, A:381 4a1a 0347 3Bout 07971, 07972, 07973, 07974, 07975, 07976 G:369, G:370, U:368 4a1a 0199 Pout 06611, 06612, 06613, 06614, 06615, 06616 A:381 4a1a 055 Pout 05443, 05444, 05445, 05446, 05447, 05448 G:259 4a1a 054 Pout 05427, 05428, 05429, 05430, 05431, 05432 U:258 4a1a 08 Pout·Rout 05059, 05060, 05061, 05062, 05063, 05064 C:238 G:236 4a1a 0334 Pout·Bout 07843, 07844, 07845, 07846, 07847, 07848 U:2140 U:2140 4a1a 079 Pout·3Bout 05603, 05604, 05605, 05606, 05607, 05608 A:23 A:24, A:25, A:26 4a1a 0345 Pout·3Bout 07955, 07956, 07957, 07958, 07959, 07960 A:289 U:270, G:271, G:290 4a1a 0204 Pout·4Bout 06675, 06676, 06677, 06678, 06679, 06680 A:374 U:376, A:3101, G:3102, A:3100 4a1a 05 2Pout 05027, 05028, 05029, 05030, 05031, 05032 G:2137, U:2136 4a1a 0325 2Pout·4Bout 07715, 07716, 07717, 07718, 07719, 07720 G:365, A:364 U:3109, G:3108, G:365, G:366 4a1a 063 2Pout·4Bout 05491, 05492, 05493, 05494, 05495, 05496 A:257, A:256 U:258, G:249, C:250, G:259

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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