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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 2otl



2OTL (2.7Å) -- RIBOSOME : Girodazole bound to the large subunit of haloarcula marismortui
List of all 61 Mg2+ binding sites in the PDB structure 2otl 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 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2otl 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03627, 07760, 09173 U:02484 G:02482, A:02532
2otl 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04345, 07738, 07739 U:02535 U:0625 U:0626
2otl 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03677, 09021, A8732
2otl 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03794, 07745, 09048, 09783 A:0455, A:0460, A:0477 A:0455
2otl 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03623, 07761, 07762 G:01837 A:01839
2otl 08006 poly-nuclear Mg2+ site U:0821(OP2), C:0822(OP2), G:0854(OP1) 03629, 03766, 09815 G:0856, U:0855
2otl 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03366, 07750, 09006 G:0833
2otl 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03641, 07754, 07837 G:02466, G:02293
2otl 08009 poly-nuclear Mg2+ site G:02611(OP1), A:02612(OP1) 03750, 07422, 07755, 07756 G:02094, G:02093
2otl 08010 Mg2+ bound by non-RNA G:0836(OP1), U:02615(OP1) 03851, 09363, B8725 GLN:B230(OE1) G:02616
2otl 08012 Oph·4Pout G:028(OP1) 03236, 03659, 07838, 09040, 09637 C:01305, U:01304, C:01343, G:01344
2otl 08013 cis-2Oph G:0877(OP1), G:02623(OP1) 03653, 03666, 07769, 09020 C:02475, A:02624 G:0885
2otl 08014 Oph·Or G:02537(OP2) G:02102(O5') 03670, 04182, 07736, 09034 G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
2otl 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03633, 07771, 09004, 09024 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
2otl 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 03757, 07763, 07764
2otl 08017 Oph·3Pout G:0456(OP2) 03955, 07746, 09417, C8555, C8657 G:0458, A:0455, U:0457
2otl 08018 cis-2Oph A:01291(OP1), G:01292(OP2) 03229, 03625, 07458, 07839 C:0910, U:0909 G:0911, G:01292
2otl 08019 Oph·2Pout A:02011(OP2) 04169, 07237, 07765, 07766, 07767 A:01941, G:01891 U:01890 G:01891, C:01892
2otl 08020 Oph·2Pout C:01830(OP1) 07749, 07768, 09119, 09122, 09195 U:01831, A:01842 G:01828 G:01828, G:01832
2otl 08021 Oph·3Pout G:02304(OP2) 03649, 03650, 07752, 07753, 09969 A:02301, A:02305, A:02303 A:02305, G:02304, U:02306

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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