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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 1s72




1S72 (2.4Å) -- RIBOSOME : Refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution
List of all 68 Mg2+ binding sites in the PDB structure 1s72 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
1s72 08110 Nb G:02609(N7) 03219, 03243, 05128, 05273, 09820 G:02609 G:02606, U:02610
1s72 08011 2Nb G:0824(N7), G:0854(N7) 03481, 03815, 03951, 04055 G:0854, G:0824, U:0823, C:0853
1s72 08084 Oph·Pout A:01742(OP2) 03156, 07350, 08769, 08893, 09274 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1s72 08039 Oph·Pout U:0115(OP2) 03488, 04624, 07318, 07319, 09431 G:0112 A:0114 A:0119, G:0118, A:0117
1s72 08036 Oph·2Pout G:0956(OP2) 03192, 07313, 07314, 07315, 08886 A:01006, A:0955 A:0957, G:0956
1s72 08020 Oph·2Pout C:01830(OP1) 07271, 07290, 08641, 08644, 08714 U:01831, A:01842 G:01828 G:01828, G:01832
1s72 08045 Oph·2Pout G:01979(OP2) 07321, 07374, 07375, 07376 G:01998, C:01999
1s72 08019 Oph·2Pout A:02011(OP2) 03675, 06750, 07287, 07288, 07289 A:01941, G:01891 U:01890 G:01891, C:01892
1s72 08068 Oph·2Pout A:02568(OP2) 03274, 04347, 05748, 07396, 09257 A:02569, G:02567 A:02569, A:02568
1s72 08083 Oph·2Pout A:01754(OP2) 03229, 03676, 05881, 07349, 07403 C:01753, A:01755 A:01755, A:01754
1s72 08037 Oph·3Pout A:02553(OP2) 03170, 07369, 08598, 09655, 09730 A:02576, U:02554, C:02575 C:02552 A:02576
1s72 08032 Oph·3Pout U:02115(OP1) 03311, 03714, 09512, A8551, A8632 U:02116, G:02272, C:02273 G:02271
1s72 08021 Oph·3Pout G:02304(OP2) 03159, 03160, 07274, 07275, 09486 A:02301, A:02305, A:02303 A:02305, G:02304, U:02306
1s72 08040 Oph·3Pout U:0392(OP2) 03312, 04168, 07371, 07372, 09213 U:0391, C:0171, U:0172
1s72 08072 Oph·3Pout U:0954(OP1) 03519, 06928, 07339, 07397, 09752 G:02299, A:02301, C:02298
1s72 08017 Oph·3Pout G:0456(OP2) 03465, 07268, 08933, C8356, C8466 G:0458, A:0455, U:0457
1s72 08012 Oph·4Pout G:028(OP1) 03169, 07360, 08559, 09156, 09747 C:01305, U:01304, C:01343, G:01344
1s72 08035 Oph·4Pout G:01484(OP2) 03238, 07311, 07312, 07367, 07368 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
1s72 08060 Oph·5Pout G:0175(OP2) 07328, 07329, 07330, 08687 C:0173, G:0225, U:0172, G:0393, U:0392
1s72 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03305, 07267, 08567, 09300 A:0455, A:0460, A:0477 A:0455

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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