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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 1vq9



1VQ9 (2.4Å) -- RIBOSOME : The structure of cca-phe-cap-bio and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui
List of all 18 Mg2+ binding sites in the PDB structure 1vq9 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
1vq9 08068 Nb A:02569(N7) 04317, 05367, 07106, E920 A:02568, A:02569 C:02565
1vq9 08075 2Or A:0907(O2'), A:0908(O4') 04200, 04480, 05474, 08254 U:01270 A:01328, A:0907
1vq9 08020 Oph·2Pout C:01830(OP1) 08190, 08209, 09740, 09743, 09814 U:01831, A:01842 G:01828 G:01828, G:01832
1vq9 08021 Oph·2Pout G:02304(OP2) 03551, 04201, 04202, 08193, 08194 A:02305, A:02303 U:02306, A:02305, G:02304
1vq9 08032 Oph·2Pout U:02115(OP1) 03575, 04750, A9586, A9666 G:02272, C:02273 G:02271
1vq9 08017 Oph·3Pout G:0456(OP2) 03027, 04507, 08187, C9167, C9270 U:0457, G:0458, A:0455
1vq9 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03366, 04349, 08186, 09671 A:0477, A:0455, A:0460 A:0455
1vq9 08027 Oph·Ob C:0240(OP1) G:0269(O6) 04438, 04577, 04715, 08281 G:0267, U:0268
1vq9 08028 Oph·Ob A:01448(OP2) U:01677(O4) 04243, 04264, 04275, S9505 G:01676
1vq9 08030 cis-2Oph U:01748(OP1), U:01749(OP2) 04203, 08188, 08189, 08199 G:02585, G:02584
1vq9 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04184, 08212, 09649, 19461 G:01688 A:0844, A:0882, A:01689, C:01690, C:01692
1vq9 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04230, A9540, A9567
1vq9 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 08216, 08217, 08218 C:02542
1vq9 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04174, 08202, 08203 G:01837 A:01839
1vq9 08002 fac-3Oph·Ob A:02483(OP1), C:02534(OP1), U:02535(OP2) G:0627(O6) 08180, 09875 C:02071
1vq9 B8056 Mg2+ bound by non-RNA A:02757(OP1) 04233, 08259, B9542, B9553 ASN:B335(O) A:02719, C:02720, G:02758
1vq9 K8069 Mg2+ bound by non-RNA 04800, 06519, K1797, K2121, K7871 ASN:K42(OD1) U:01749, A:02583, G:02584, U:02546
1vq9 08079 poly-nuclear Mg2+ site A:0167(OP1), C:0168(OP2) A:0165(N7) 04173, 04179, 04191 G:0164, A:0165 G:0164

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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