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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 1vqm



1VQM (2.3Å) -- RIBOSOME : The structure of the transition state analogue "dan" bound to the large ribosomal subunit of haloarcula marismortui
List of all 24 Mg2+ binding sites in the PDB structure 1vqm 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
1vqm 08068 Nb A:02569(N7) 04348, 05393, 07183, E920 A:02568, A:02569 C:02565 G:02570
1vqm 08084 Oph·Pout A:01742(OP2) 03367, 04234, 08375 G:02033 G:02033, G:01743, G:01744, G:01745, A:01742
1vqm 08019 Oph·2Pout A:02011(OP2) 04741, 07724, 08316, 08317 A:01941, G:01891 U:01890 G:01891, C:01892
1vqm 08020 Oph·2Pout C:01830(OP1) 08299, 08318, 09747, 09750, 09822 U:01831, A:01842 G:01828 G:01828, G:01832
1vqm 08032 Oph·3Pout U:02115(OP1) 03600, 04384, 04778, 08334, A9539 G:02272, C:02273, U:02116 G:02271
1vqm 08017 Oph·3Pout G:0456(OP2) 03043, 08296, C9164, C9168, C9271 U:0457, G:0458, A:0455
1vqm 08036 Oph·3Pout G:0956(OP2) 04268, 08337, 08338, 08339, 09993 A:01006, A:0955, A:0957 G:0956, A:0957
1vqm 08012 Oph·4Pout G:028(OP1) 03258, 03833, 04246, 08385, 09664 C:01343, G:01344, C:01305, U:01304
1vqm 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03391, 04379, 08295, 09672 A:0477, A:0455, A:0460 A:0455
1vqm 08027 Oph·Ob C:0240(OP1) G:0269(O6) 04467, 04605, 04746, 08390 G:0267, U:0268
1vqm 08028 Oph·Ob A:01448(OP2) U:01677(O4) 04276, 04297, 04308, 08328 G:01676
1vqm 08054 cis-2Oph C:0162(OP1), U:02276(OP1) 03060, 08301, 08348, 08349 A:0169, U:0163
1vqm 08030 cis-2Oph U:01748(OP1), U:01749(OP2) 04239, 08297, 08298, 08308 G:02585, G:02584
1vqm 08074 cis-2Oph A:01286(OP1), A:01287(OP1) 08361, 08362, W7873, W7874 A:01287
1vqm 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04222, 08320, 09633, 09650 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1vqm 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 08288, 08289, 09886 U:02535, G:02482 U:0625
1vqm 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04264, A9500, A9523
1vqm 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 03022, 08324, 08325
1vqm 08118 mer-3Oph A:02637(OP1), DA:4179(OP1), C:4180(OP1) 08448, 08449, 47911 C:02636, U:02620 A:02474
1vqm 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04212, 08311, 08312 G:01837 A:01839

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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