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 4a1c 4A1C (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 4. List of all 11 Mg2+ binding sites in the PDB structure 4a1c 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 4a1c 0347 2Bout 07443, 07444, 07445, 07446, 07447, 07448 G:369, G:370 4a1c 0117 3Bout 05619, 05620, 05621, 05622, 05623, 05624 G:382, G:383, A:381 4a1c 066 3Bout 05331, 05332, 05333, 05334, 05335, 05336 G:215, G:216, U:217 4a1c 054 Pout 05251, 05252, 05253, 05254, 05255, 05256 U:258 4a1c 08 Pout·2Rout 05027, 05028, 05029, 05030, 05031, 05032 A:237 G:236, A:237 4a1c 0345 Pout·2Bout 07411, 07412, 07413, 07414, 07415, 07416 A:289 G:271, G:290 4a1c 0204 Pout·4Bout 06291, 06292, 06293, 06294, 06295, 06296 A:374 U:376, A:3101, G:3102, A:3100 4a1c 070 2Pout 05347, 05348, 05349, 05350, 05351, 05352 A:25, A:24 4a1c 0325 2Pout·3Bout 07219, 07220, 07221, 07222, 07223, 07224 G:365, A:364 U:3109, G:365, G:366 4a1c 01 2Pout·3Bout 05011, 05012, 05013, 05014, 05015, 05016 U:2148, G:2149 G:2147, G:2149, U:2150 4a1c 063 2Pout·3Bout 05299, 05300, 05301, 05302, 05303, 05304 A:257, A:256 U:258, C:250, G:249

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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