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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 1qvf




1QVF (3.1Å) -- RIBOSOME : Structure of a deacylated trna minihelix bound to the e site of the large ribosomal subunit of haloarcula marismortui
List of all 63 Mg2+ binding sites in the PDB structure 1qvf 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
1qvf 08084 Oph·Pout A:01742(OP2) 03151, 08772, 08895, 09273 G:02033 G:01744, G:01745, G:01743, G:02033
1qvf 08083 Oph·Pout A:01754(OP2) 03223, 03663, 05842, 07295, 07345 C:01753 A:01755, A:01754
1qvf 08051 Oph·Pout G:0641(OP2) 03614, 07268, 07269 A:01355 A:01355, G:0642, G:0641
1qvf 08039 Oph·Pout U:0115(OP2) 03476, 04595, 07264, 07265, 09429 G:0112 A:0114 A:0119, G:0118, A:0117
1qvf 08020 Oph·2Pout C:01830(OP1) 07220, 07237, 08643, 08646, 08720 U:01831, A:01842 G:01828 G:01828, G:01832
1qvf 08068 Oph·2Pout A:02568(OP2) 03266, 04316, 05710, 07340, 09256 A:02569, G:02567 A:02569, A:02568
1qvf 08019 Oph·2Pout A:02011(OP2) 03662, 06709, 07234, 07235, 07236 A:01941, G:01891 U:01890 G:01891, C:01892
1qvf 08092 Oph·2Pout C:01844(OP2) 03161, 03175, 07348 A:01843, A:01845 A:01845
1qvf 08045 Oph·2Pout G:01979(OP2) 07267, 07318, 07319, 07320 G:01998, C:01999
1qvf 08037 Oph·3Pout A:02553(OP2) 03165, 07313, 08599, 09652, 09726 A:02576, U:02554, C:02575 C:02552 A:02576
1qvf 08035 Oph·3Pout G:01484(OP2) 03231, 07257, 07258, 07311, 07312 C:01456, A:01485, C:01455 G:01484, U:01457
1qvf 08032 Oph·3Pout U:02115(OP1) 03241, 03302, 03700, 09506, A8629 U:02116, G:02272, C:02273
1qvf 08017 Oph·3Pout G:0456(OP2) 03456, 07217, 08934, C8357, C8460 G:0458, A:0455, U:0457
1qvf 08040 Oph·3Pout U:0392(OP2) 03303, 04144, 07315, 07316, 09213 U:0391, C:0171, U:0172
1qvf 08091 Oph·3Pout G:0918(OP1) 05964, 07299, 08614, 09068, 09841 C:02294, C:02391, A:02465 A:02465
1qvf 08021 Oph·3Pout G:02304(OP2) 03154, 03155, 07222, 07223, 09482 A:02301, A:02303, A:02305 A:02305, G:02304, U:02306
1qvf 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03385, 03525, 03667, L8643 G:0267, U:0268
1qvf 08110 Oph·Nb U:0903(OP1) A:01357(N7) 03438, 04886, 05519, 09029 U:0904 G:0622, A:01356
1qvf 08014 cis-2Oph G:02102(OP2), G:02537(OP2) 03174, 03675, 07207, 08552 C:02536, A:02101 G:02480, G:02481, A:02101
1qvf 08013 cis-2Oph G:0877(OP1), G:02623(OP1) 03158, 03170, 08540, A8628 C:02475, A:02624 G:0885

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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