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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 1vq7



1VQ7 (2.5Å) -- RIBOSOME : The structure of the transition state analogue "dca" bound to the large ribosomal subunit of haloarcula marismortui
List of all 63 Mg2+ binding sites in the PDB structure 1vq7 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
1vq7 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03939, 07986, 09504 U:02484 G:02482, A:02532
1vq7 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04649, 07964, 07965 U:02535 U:0625 U:0626
1vq7 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03990, 09341, A9332
1vq7 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03100, 04106, 07971, 09368 A:0477, A:0455, A:0460 A:0455
1vq7 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03935, 07987, 07988 G:01837 A:01839
1vq7 08006 fac-3Oph U:0821(OP2), C:0822(OP2), G:0854(OP1) 03131, 03941, 04078 U:0855, G:0856
1vq7 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03679, 07976, 09328 G:0833
1vq7 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03953, 07980, 08169 G:02466, G:02293
1vq7 08009 cis-2Oph G:02611(OP1), A:02612(OP1) 04062, 07655, 07981, 07982 G:02094, G:02093
1vq7 08010 Mg2+ bound by non-RNA G:0836(OP1), U:02615(OP1) 04163, 09688, B9324 GLN:B230(OE1) G:02616
1vq7 08011 2Nb G:0824(N7), G:0854(N7) 04283, 04616, 04746, 04847 G:0854, U:0823, G:0824, C:0853
1vq7 08012 Oph·4Pout G:028(OP1) 03549, 03972, 08170, 09360, 09960 C:01305, U:01304, C:01343, G:01344
1vq7 08013 cis-2Oph G:0877(OP1), G:02623(OP1) 03966, 03979, 09340, A9422 C:02475, A:02624 G:0885
1vq7 08014 cis-2Oph G:02102(OP2), G:02537(OP2) 03983, 04491, 07962, 09354 G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
1vq7 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03945, 07995, 09326, 09344 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1vq7 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 04069, 07989, 07990
1vq7 08017 Oph·3Pout G:0456(OP2) 04268, 07622, 07972, 09740, C9155 G:0458, A:0455, U:0457
1vq7 08018 cis-2Oph A:01291(OP1), G:01292(OP2) 03543, 03937, 07690, 08171 C:0910, U:0909 G:0911, G:01292
1vq7 08019 Oph·2Pout A:02011(OP2) 04477, 07474, 07991, 07992, 07993 A:01941, G:01891 U:01890 G:01891, C:01892
1vq7 08020 Oph·2Pout C:01830(OP1) 07975, 07994, 09448, 09451, 09525 U:01831, A:01842 G:01828 G:01828, G:01832

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>