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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 1yij



1YIJ (2.6Å) -- RIBOSOME : Crystal structure of telithromycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
List of all 63 Mg2+ binding sites in the PDB structure 1yij 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
1yij 08110 Nb G:02609(N7) 03309, 03706, 03730, 05612, 05757 G:02609 U:02610, G:02606
1yij 08011 2Nb G:0824(N7), G:0854(N7) 03970, 04307, 04439, 04544 G:0854, G:0824, U:0823, C:0853
1yij 08039 Oph·Pout U:0115(OP2) 03976, 05110, 07786, 07787, 09917 G:0112 A:0114 A:0119, G:0118
1yij 08084 Oph·Pout A:01742(OP2) 03644, 07818, 09250, 09377, 09755 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1yij 08019 Oph·2Pout A:02011(OP2) 04166, 07225, 07754, 07755, 07756 A:01941, G:01891 U:01890 G:01891, C:01892
1yij 08068 Oph·2Pout A:02568(OP2) 03761, 04834, 06222, 07864, 09737 A:02569, G:02567 A:02569, A:02568
1yij 08083 Oph·2Pout A:01754(OP2) 03716, 04167, 06354, 07817, 07869 C:01753, A:01755 A:01755, A:01754
1yij 08020 Oph·2Pout C:01830(OP1) 07738, 07757, 09123, 09126, 09198 U:01831, A:01842 G:01828 G:01828, G:01832
1yij 08037 Oph·3Pout A:02553(OP2) 03146, 03219, 03658, 07837, 09078 A:02576, C:02575, U:02554 C:02552 A:02576
1yij 08036 Oph·3Pout G:0956(OP2) 03679, 07781, 07782, 07783, 09371 A:01006, A:0955, A:0957 A:0957, G:0956
1yij 08035 Oph·3Pout G:01484(OP2) 03725, 07779, 07780, 07835, 07836 C:01456, A:01485, C:01455 G:01484, U:01457
1yij 08032 Oph·3Pout U:02115(OP1) 03799, 04205, 07777, 09996, A8845 U:02116, G:02272, C:02273
1yij 08017 Oph·3Pout G:0456(OP2) 03955, 07381, 07735, 09418, C8562 G:0458, A:0455, U:0457
1yij 08040 Oph·3Pout U:0392(OP2) 03800, 04660, 07839, 07840, 09694 U:0391, C:0171, U:0172
1yij 08072 Oph·3Pout U:0954(OP1) 03241, 04008, 07403, 07807, 07865 C:02298, G:02299, A:02301
1yij 08021 Oph·3Pout G:02304(OP2) 03647, 03648, 07741, 07742, 09970 A:02301, A:02305, A:02303 A:02305, G:02304, U:02306
1yij 08012 Oph·4Pout G:028(OP1) 03236, 03657, 07828, 09038, 09640 C:01305, U:01304, C:01343, G:01344
1yij 08091 Oph·5Pout G:0918(OP1) 03334, 06483, 07822, 09093, 09549 G:02293, C:02294, C:02391, A:02465, U:0919 A:02465
1yij 08014 Oph·Or G:02537(OP2) G:02102(O5') 03668, 04179, 07725, 09032 G:02102, G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
1yij 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03793, 07734, 09046, 09782 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/)
For any help please contact <dust@iwonka.med.virginia.edu>