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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 08068 Oph·Pout A:02568(OP2) 03764, 04844, 07873, 09740, E5607 G:02567 A:02569, A:02568
2otl 08084 Oph·Pout A:01742(OP2) 03646, 07828, 09250, 09375, 09757 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
2otl 08039 Oph·Pout U:0115(OP2) 03977, 05121, 07796, 09917 G:0112 A:0114 A:0119, G:0118
2otl 08092 Oph·Pout C:01844(OP2) 03656, 03671, 07882, 09387 A:01843 A:01845
2otl 08019 Oph·2Pout A:02011(OP2) 04169, 07237, 07765, 07766, 07767 A:01941, G:01891 U:01890 G:01891, C:01892
2otl 08059 Oph·2Pout G:02618(OP1) 03733, 04064, 07759, 09039, 09043 C:02641, G:02642 G:02643, G:02642
2otl 08083 Oph·2Pout A:01754(OP2) 03718, 04170, 06364, 07827, 07879 C:01753, A:01755 A:01755, A:01754
2otl 08020 Oph·2Pout C:01830(OP1) 07749, 07768, 09119, 09122, 09195 U:01831, A:01842 G:01828 G:01828, G:01832
2otl 08037 Oph·3Pout A:02553(OP2) 03142, 03219, 03660, 07847, 09078 C:02575, A:02576, U:02554 C:02552 A:02576
2otl 08036 Oph·3Pout G:0956(OP2) 03681, 07791, 07792, 07793, 09369 A:01006, A:0955, A:0957 A:0957, G:0956
2otl 08035 Oph·3Pout G:01484(OP2) 03727, 07789, 07790, 07845, 07846 C:01456, A:01485, C:01455 G:01484, U:01457
2otl 08032 Oph·3Pout U:02115(OP1) 03800, 04209, 09996, A8749, A8824 U:02116, G:02272, C:02273
2otl 08017 Oph·3Pout G:0456(OP2) 03955, 07746, 09417, C8555, C8657 G:0458, A:0455, U:0457
2otl 08040 Oph·3Pout U:0392(OP2) 03801, 04663, 07849, 07850, 09695 U:0391, C:0171, U:0172
2otl 08021 Oph·3Pout G:02304(OP2) 03649, 03650, 07752, 07753, 09969 A:02301, A:02305, A:02303 A:02305, G:02304, U:02306
2otl 08012 Oph·4Pout G:028(OP1) 03236, 03659, 07838, 09040, 09637 C:01305, U:01304, C:01343, G:01344
2otl 08091 Oph·5Pout G:0918(OP1) 03333, 06486, 07832, 09092, 09550 G:02293, C:02294, C:02391, A:02465, U:0919 A:02465
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 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03883, 04027, 04174, 07843 G:0267, U:0268
2otl 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03794, 07745, 09048, 09783 A:0455, A:0460, A:0477 A:0455

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].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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