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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 1yi2



1YI2 (2.65Å) -- RIBOSOME : Crystal structure of erythromycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
List of all 66 Mg2+ binding sites in the PDB structure 1yi2 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
1yi2 08110 Nb G:02609(N7) 03301, 03694, 03718, 05586, 05733 G:02609 U:02610, G:02606
1yi2 08051 Oph·Pout G:0641(OP2) 04099, 07778, 07779 A:01355 G:0642, A:01355
1yi2 08084 Oph·Pout A:01742(OP2) 03632, 07805, 09249, 09376, 09754 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1yi2 08039 Oph·Pout U:0115(OP2) 03962, 05086, 07774, 07775, 09916 G:0112 A:0114 A:0119, G:0118, A:0117
1yi2 08037 Oph·2Pout A:02553(OP2) 03138, 03213, 03646, 07824, 09077 C:02575, U:02554 C:02552 A:02576
1yi2 08020 Oph·2Pout C:01830(OP1) 07726, 07745, 09121, 09124, 09195 U:01831, A:01842 G:01828 G:01828, G:01832
1yi2 08052 Oph·2Pout U:01125(OP1) 03621, 07849, 98590, 98616 C:01126, G:992 C:01129, G:990
1yi2 08019 Oph·2Pout A:02011(OP2) 04146, 07211, 07742, 07743, 07744 A:01941, G:01891 U:01890 G:01891, C:01892
1yi2 08068 Oph·2Pout A:02568(OP2) 03749, 04811, 06208, 07851, 09736 A:02569, G:02567 A:02569, A:02568
1yi2 08083 Oph·2Pout A:01754(OP2) 03704, 04147, 06340, 07804, 07857 C:01753, A:01755 A:01755, A:01754
1yi2 08036 Oph·3Pout G:0956(OP2) 03667, 07769, 07770, 07771, 09370 A:01006, A:0955, A:0957 A:0957, G:0956
1yi2 08032 Oph·3Pout U:02115(OP1) 03786, 04185, 09993, A8848, A8926 U:02116, G:02272, C:02273
1yi2 08021 Oph·3Pout G:02304(OP2) 03635, 03636, 07729, 07730, 09969 A:02301, A:02305, A:02303 A:02305, G:02304, U:02306
1yi2 08040 Oph·3Pout U:0392(OP2) 03787, 04636, 07826, 07827, 09693 U:0391, C:0171, U:0172
1yi2 08072 Oph·3Pout U:0954(OP1) 03234, 03993, 07387, 07794, 07852 C:02298, G:02299, A:02301
1yi2 08017 Oph·3Pout G:0456(OP2) 03941, 07364, 07723, 09416, C8558 G:0458, A:0455, U:0457
1yi2 08035 Oph·4Pout G:01484(OP2) 03713, 07767, 07768, 07822, 07823 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
1yi2 08091 Oph·4Pout G:0918(OP1) 03325, 06465, 07809, 09091, 09549 G:02293, C:02294, A:02465, U:0919 A:02465
1yi2 08012 Oph·4Pout G:028(OP1) 03229, 03645, 07815, 09037, 09639 C:01305, U:01304, C:01343, G:01344
1yi2 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03780, 07722, 09045, 09781 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>