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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 1vq5



1VQ5 (2.6Å) -- RIBOSOME : The structure of the transition state analogue "raa" bound to the large ribosomal subunit of haloarcula marismortui
List of all 67 Mg2+ binding sites in the PDB structure 1vq5 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
1vq5 08107 cis-2Oph A:01106(OP2), A:01107(OP2) 08196, 08197, 08198, 08199 C:01103, C:01104 C:01105 A:01107
1vq5 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03938, 08161, 08162, 09564 A:0882, C:0884 U:0883, A:01836
1vq5 98052 trans-2Oph U:01125(OP1), G:93092(OP1) 03939, 08207, 9737, 92357 C:01126 C:01129, G:93090
1vq5 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03937, 08052, 09345, 19203 G:01688 A:0844, A:01689, C:01690, C:01692, A:0882
1vq5 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04637, 07969, 07970 U:02535 U:0625 U:0626
1vq5 08079 cis-2Oph·Nb A:0167(OP1), C:0168(OP2) A:0165(N7) 03926, 03932, 03944 G:0164, A:0165 G:0164
1vq5 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 04060, 07994, 07995
1vq5 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 08069, 08073, 09718 C:02542
1vq5 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03982, 09342, A9328
1vq5 08006 fac-3Oph U:0821(OP2), C:0822(OP2), G:0854(OP1) 03130, 03933, 04068 U:0855, G:0856
1vq5 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03931, 07991, 09500 U:02484 A:02532, G:02482
1vq5 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 04413, 09935 U:01422
1vq5 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03927, 07992, 07993 G:01837 A:01839
1vq5 48118 mer-3Oph A:02637(OP1), A:4176(OP1), C:4175(OP1) 08230, 47901, 47902 U:02620, C:02636 A:02474
1vq5 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03676, 07981, 09328 G:0833
1vq5 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03945, 07985, 08174 G:02466, G:02293
1vq5 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03003, 04131 U:02586
1vq5 08063 2Bout 04495, 07257, 07667, 07975, 08157 G:01364, G:01363
1vq5 08038 6Bout 03941, 03966, 03987, 03989, 08132, 09605 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1vq5 A8065 Pout·Rout 03248, 04282, A9320, A9344, A9395, A9424 C:0783 G:0782

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>