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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 1jj2




1JJ2 (2.4Å) -- RIBOSOME : Fully refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution
List of all 71 Mg2+ binding sites in the PDB structure 1jj2 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
1jj2 08112 Nb A:0187(N1) 03254, 03295, 08648, 08851, 09088 U:0207, C:0155 G:0206 C:0438, C:0188
1jj2 08111 Nb G:02609(N7) 03224, 03248, 05142, 05289, 09825 G:02609 G:02606, U:02610
1jj2 08097 2Ob G:0863(O6), U:0864(O4) 03199, 03203, 05094, 09865 U:0862, G:0782
1jj2 08011 2Nb G:0824(N7), G:0854(N7) 03487, 03819, 03956, 04061 G:0854, G:0824, U:0823, C:0853
1jj2 08039 Oph·Pout U:0115(OP2) 03493, 04637, 07363, 07364, 09434 G:0112 A:0114 A:0119, G:0118, A:0117
1jj2 08084 Oph·Pout A:01742(OP2) 03161, 07395, 08769, 08893, 09276 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1jj2 08020 Oph·2Pout C:01830(OP1) 07316, 07335, 08641, 08644, 08715 U:01831, A:01842 G:01828 G:01828, G:01832
1jj2 08068 Oph·2Pout A:02568(OP2) 03279, 04357, 05768, 07441, 09259 A:02569, G:02567 A:02569, A:02568
1jj2 08019 Oph·2Pout A:02011(OP2) 03678, 06783, 07332, 07333, 07334 A:01941, G:01891 U:01890 G:01891, C:01892
1jj2 08083 Oph·2Pout A:01754(OP2) 03234, 03679, 05901, 07394, 07448 C:01753, A:01755 A:01755, A:01754
1jj2 08045 Oph·2Pout G:01979(OP2) 07366, 07418, 07419, 07420 G:01998, C:01999
1jj2 08036 Oph·2Pout G:0956(OP2) 03197, 07358, 07359, 07360, 08886 A:01006, A:0955 A:0957, G:0956
1jj2 08037 Oph·3Pout A:02553(OP2) 03175, 07413, 08598, 09659, 09734 A:02576, U:02554, C:02575 C:02552 A:02576
1jj2 08032 Oph·3Pout U:02115(OP1) 03315, 03717, 09515, A8551, A8631 U:02116, G:02272, C:02273 G:02271
1jj2 08021 Oph·3Pout G:02304(OP2) 03164, 03165, 07319, 07320, 09489 A:02301, A:02305, A:02303 A:02305, G:02304, U:02306
1jj2 08072 Oph·3Pout U:0954(OP1) 03524, 06966, 07384, 07442, 09756 G:02299, A:02301, C:02298
1jj2 08040 Oph·3Pout U:0392(OP2) 03316, 04178, 07415, 07416, 09216 U:0391, C:0171, U:0172
1jj2 08017 Oph·3Pout G:0456(OP2) 03471, 07313, 08933, C8358, C8466 G:0458, A:0455, U:0457
1jj2 08012 Oph·4Pout G:028(OP1) 03174, 07405, 08559, 09158, 09751 C:01305, U:01304, C:01343, G:01344
1jj2 08035 Oph·4Pout G:01484(OP2) 03243, 07356, 07357, 07411, 07412 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457

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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