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 4a17 4A17 (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 2. List of all 17 Mg2+ binding sites in the PDB structure 4a17 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 4a17 08 Rout 05075, 05076, 05077, 05078, 05079, 05080 A:237 4a17 0334 Bout 08499, 08500, 08501, 08502, 08503, 08504 G:2141 4a17 071 Bout 05715, 05716, 05717, 05718, 05719, 05720 U:210 4a17 0117 2Bout 06147, 06148, 06149, 06150, 06151, 06152 G:382, G:383 4a17 066 3Bout 05635, 05636, 05637, 05638, 05639, 05640 G:215, G:216, U:217 4a17 0203 4Bout 07043, 07044, 07045, 07046, 07047, 07048 U:396, G:397, U:395, U:379 4a17 0199 Pout 06979, 06980, 06981, 06982, 06983, 06984 A:381 4a17 070 Pout 05699, 05700, 05701, 05702, 05703, 05704 A:25 4a17 079 Pout 05811, 05812, 05813, 05814, 05815, 05816 A:24 4a17 055 Pout 05539, 05540, 05541, 05542, 05543, 05544 G:259 4a17 01 Pout·2Bout 05011, 05012, 05013, 05014, 05015, 05016 U:2148 G:2147, G:2149 4a17 0324 Pout·2Bout 08355, 08356, 08357, 08358, 08359, 08360 A:316 A:316, A:317 4a17 0345 Pout·2Bout 08643, 08644, 08645, 08646, 08647, 08648 A:269 U:270, G:290 4a17 0204 Pout·3Bout 07059, 07060, 07061, 07062, 07063, 07064 A:374 U:376, A:3101, A:3100 4a17 05 2Pout·2Bout 05043, 05044, 05045, 05046, 05047, 05048 G:2137, U:2136 G:2137, U:2138 4a17 063 2Pout·4Bout 05603, 05604, 05605, 05606, 05607, 05608 A:257, A:256 U:258, G:259, G:249, C:250 4a17 0325 3Pout·4Bout 08371, 08372, 08373, 08374, 08375, 08376 G:365, G:366, A:364 U:3109, G:3108, G:365, G:366

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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