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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 1qvg




1QVG (2.9Å) -- RIBOSOME : Structure of cca oligonucleotide bound to the trna binding sites of the large ribosomal subunit of haloarcula marismortui
List of all 47 Mg2+ binding sites in the PDB structure 1qvg 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 3 | « Previous | | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1qvg 08102 Ob·Nb A:02434(N3), U:02458(O2) 07288, 08778, 09399, 28518 A:02434, U:02458
1qvg 08051 Oph·Pout G:0641(OP2) 03600, 07201, 07202 A:01355 A:01355, G:0642, G:0641
1qvg 08058 Oph·2Pout G:02013(OP2) 07204, 07205, A8622, A8624 U:01883, C:02626
1qvg 08092 Oph·2Pout C:01844(OP2) 03151, 03166, 07278, 08908 A:01843, A:01845 A:01845
1qvg 08019 Oph·2Pout A:02011(OP2) 03647, 06645, 07168, 07169, 07170 A:01941, G:01891 U:01890 G:01891
1qvg 08052 Oph·2Pout U:01125(OP1) 03128, 03357, 98390, 98530 C:01126, G:93092 C:01129, G:93090
1qvg 08068 Oph·2Pout A:02568(OP2) 03257, 04300, 05662, 07270, E920 A:02569, G:02567 A:02569, A:02568
1qvg 08083 Oph·2Pout A:01754(OP2) 03212, 03648, 05791, 07227, 07275 C:01753, A:01755 A:01755, A:01754
1qvg 08020 Oph·2Pout C:01830(OP1) 07153, 07171, 08644, 08647, 08721 U:01831, A:01842 G:01828 G:01828, A:01845, G:01832
1qvg 08039 Oph·2Pout U:0115(OP2) 03463, 04578, 07197, 09416 G:0112, G:0116 A:0114 A:0119, A:0117, G:0118
1qvg 08032 Oph·3Pout U:02115(OP1) 03231, 03292, 03685, 09496, A8621 U:02116, G:02272, C:02273
1qvg 08037 Oph·3Pout A:02553(OP2) 03154, 07245, 08602, 09641, 09716 A:02576, U:02554, C:02575 C:02552 A:02576
1qvg 08021 Oph·3Pout G:02304(OP2) 03144, 03145, 07155, 07156, 09469 A:02301, A:02303, A:02305 A:02305, G:02304, U:02306
1qvg 08040 Oph·3Pout U:0392(OP2) 03293, 04123, 07247, 07248, 09208 U:0391, C:0171, U:0172
1qvg 08091 Oph·4Pout G:0918(OP1) 05909, 07232, 08616, 09065, 09830 C:02294, C:02391, A:02465, U:0919 A:02465
1qvg 08035 Oph·4Pout G:01484(OP2) 03221, 07189, 07190, 07243, 07244 C:01483, C:01455, C:01456, A:01485 U:01457
1qvg 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03374, 03510, 03652, L8645 G:0267, U:0268
1qvg 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03137, 03457, 05612, 08918 G:01490, A:01487, U:01488 G:01489, G:01490
1qvg 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03286, 07149, 08569, 09287 A:0455, A:0460, A:0477 A:0455
1qvg 08013 cis-2Oph G:0877(OP1), G:02623(OP1) 03148, 03160, 08542, A8620 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].


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