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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 1vq8



1VQ8 (2.2Å) -- RIBOSOME : The structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui
List of all 26 Mg2+ binding sites in the PDB structure 1vq8 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1vq8 08020 Oph·2Pout C:01830(OP1) 08293, 08312, 09747, 09750, 09821 U:01831, A:01842 G:01828 G:01828, G:01832
1vq8 08019 Oph·2Pout A:02011(OP2) 04737, 07715, 08309, 08310, 08311 A:01941, G:01891 U:01890 G:01891, C:01892
1vq8 08032 Oph·2Pout U:02115(OP1) 03600, 04774, A9540, A9614 G:02272, C:02273
1vq8 08017 Oph·3Pout G:0456(OP2) 03038, 04532, 08290, C9162, C9265 U:0457, G:0458, A:0455
1vq8 08036 Oph·3Pout G:0956(OP2) 04263, 08333, 08334, 08335, 09988 A:01006, A:0955, A:0957 G:0956, A:0957
1vq8 08012 Oph·4Pout G:028(OP1) 03256, 03828, 04240, 08380, 09665 C:01343, G:01344, C:01305, U:01304
1vq8 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03393, 04374, 08289, 09673 A:0477, A:0455, A:0460 A:0455
1vq8 08027 Oph·Ob C:0240(OP1) G:0269(O6) 04463, 04604, 04742, 08385 G:0267, U:0268
1vq8 08028 Oph·Ob A:01448(OP2) U:01677(O4) 04271, 04292, 04303, 08323 G:01676
1vq8 08070 Oph·Ob A:0166(OP1) G:0219(O6) 04406, 05525, 06148, 09748 A:0165, G:0221 G:0221
1vq8 08084 Oph·Nb A:01742(OP2) G:02033(N7) 03369, 04227, 08370 G:02033 G:01743, G:01744, G:01745, A:01742
1vq8 08110 Oph·Nb U:0903(OP1) A:01357(N7) 04515, 05964, 06570 U:0904 G:0622
1vq8 08054 cis-2Oph C:0162(OP1), U:02276(OP1) 03056, 08295, 08344, 08345 A:0169, U:0163
1vq8 08030 cis-2Oph U:01748(OP1), U:01749(OP2) 04232, 08291, 08292, 08302 G:02585, G:02584
1vq8 08074 cis-2Oph A:01286(OP1), A:01287(OP1) 08356, 08357, W7873, W7874 A:01287
1vq8 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04214, 08315, 09633, 09651 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1vq8 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 08282, 08283, 09881 U:02535 U:0625, G:02482 C:02071
1vq8 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04259, 09648, A9522
1vq8 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 03016, 08319, 08320 C:02542
1vq8 08029 fac-3Oph U:01503(OP1), A:01504(OP2), C:01679(OP1) 03817, 08325, 08327

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>