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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 1yjw



1YJW (2.9Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of quinupristin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
List of all 61 Mg2+ binding sites in the PDB structure 1yjw 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
1yjw 78110 Nb G:02609(N7) 04789, 09357, 09358, 09375, 09378 G:02609 G:02606, U:02610
1yjw 78097 2Ob G:0863(O6), U:0864(O4) 05757, 05969, 05977, 05980 G:0782, U:0862
1yjw 78011 2Nb G:0824(N7), G:0854(N7) 05841, 05842, 05941, 05943 U:0823, G:0824, G:0854
1yjw 78019 Oph·2Pout A:02011(OP2) 08084, 08085, 08123, 08234 G:01891, A:01941 U:01890 G:01891
1yjw 78072 Oph·2Pout U:0954(OP1) 06233, 08673, 08675, 08681, 08684 C:02298, A:02301
1yjw 78020 Oph·2Pout C:01830(OP1) 07913, 07918, 07919, 07921, 07953 A:01842, U:01831 G:01828 G:01828, G:01832
1yjw 78068 Oph·2Pout A:02568(OP2) 09263, 09265, 09268, 09269, E4036 G:02567, A:02569 A:02568, A:02569
1yjw 78083 Oph·2Pout A:01754(OP2) 07792, 07794, 07797, 07800, 07803 C:01753, A:01755 A:01754, A:01755
1yjw 78017 Oph·3Pout G:0456(OP2) 05094, 05099, 05100, 05103, C4068 A:0455, U:0457, G:0458
1yjw 78037 Oph·3Pout A:02553(OP2) 09244, 09245, 09246, 09248, 09281 U:02554, A:02576, C:02575 C:02552 A:02576
1yjw 78036 Oph·3Pout G:0956(OP2) 06242, 06243, 06245, 06246, 06278 A:0955, A:01006, A:0957 G:0956, A:0957
1yjw 78032 Oph·3Pout U:02115(OP1) 08514, 08601, 08602, A4081, A4082 C:02273, U:02116, G:02272 G:02271
1yjw 78021 Oph·3Pout G:02304(OP2) 08688, 08696, 08699, 08701, 08704 A:02303, A:02301, A:02305 G:02304, A:02305, U:02306
1yjw 78091 Oph·4Pout G:0918(OP1) 06150, 08660, 08668, 09021, 09022 C:02294, A:02465, C:02391, U:0919 G:02397, A:02465
1yjw 78035 Oph·5Pout G:01484(OP2) 07233, 07235, 07237, 07289, 07290 C:01455, C:01456, U:01457, A:01485, C:01483 U:01457, G:01484
1yjw 78014 Oph·Or G:02537(OP2) G:02102(O5') 08468, 09071, 09188, 09190 G:02102, G:02481 A:02101, C:02536 A:02101, G:02480, G:02481
1yjw 78062 Oph·Ob G:01489(OP2) G:01491(O6) 07298, 07300, 07304, 07305 A:01487, U:01488, G:01490 G:01490, G:01489
1yjw 78028 Oph·Ob A:01448(OP2) U:01677(O4) 07211, 07214, 07573, S4022 G:01676
1yjw 78027 Oph·Ob C:0240(OP1) G:0269(O6) 04761, 04763, 04822, 04823 G:0267, U:0268
1yjw 78004 Oph·Ob A:0459(OP1) G:0456(O6) 05092, 05093, 05096, 05106 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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