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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 1vq4




1VQ4 (2.7Å) -- RIBOSOME : The structure of the transition state analogue "daa" bound to the large ribosomal subunit of haloarcula marismortui
List of all 58 Mg2+ binding sites in the PDB structure 1vq4 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
1vq4 08011 2Nb G:0824(N7), G:0854(N7) 04265, 04597, 04724, 04824 G:0854, U:0823, G:0824, C:0853
1vq4 08039 Oph·Pout U:0115(OP2) 03226, 04271, 05397, 07982, 07983 G:0112 G:0118, A:0119, A:0117
1vq4 08068 Oph·Pout A:02568(OP2) 04056, 05124, 08164, E920, E5607 G:02567 A:02569, A:02568
1vq4 08084 Oph·Pout A:01742(OP2) 03067, 03940, 08121, 09569, 09694 G:02033 G:02033, G:01744, G:01745, A:01742, G:01743
1vq4 08083 Oph·2Pout A:01754(OP2) 04011, 04462, 06613, 08120, 08170 C:01753, A:01755 A:01755, A:01754
1vq4 08020 Oph·2Pout C:01830(OP1) 07935, 07954, 09440, 09443, 09516 U:01831, A:01842 G:01828 G:01828, G:01832
1vq4 08019 Oph·2Pout A:02011(OP2) 04461, 07442, 07951, 07952, 07953 A:01941, G:01891 U:01890 G:01891, C:01892
1vq4 08036 Oph·3Pout G:0956(OP2) 03975, 07977, 07978, 07979, 09688 A:01006, A:0955, A:0957 A:0957, G:0956
1vq4 08037 Oph·3Pout A:02553(OP2) 03445, 03517, 03954, 08139, 09397 C:02575, A:02576, U:02554 C:02552 A:02576
1vq4 08017 Oph·3Pout G:0456(OP2) 03926, 04250, 07932, 09735, C9267 A:0455, G:0458, U:0457
1vq4 08035 Oph·3Pout G:01484(OP2) 04020, 07975, 07976, 08137, 08138 C:01455, C:01456, A:01485 G:01484, U:01457
1vq4 08032 Oph·3Pout U:02115(OP1) 03304, 04093, 04499, A9347, A9421 C:02273, U:02116, G:02272
1vq4 08021 Oph·3Pout G:02304(OP2) 03278, 03943, 03944, 07938, 07939 A:02301, A:02303, A:02305 U:02306, A:02305, G:02304
1vq4 08040 Oph·3Pout U:0392(OP2) 03010, 04094, 04941, 08141, 08142 U:0172, U:0391, C:0171
1vq4 08012 Oph·4Pout G:028(OP1) 03534, 03953, 08131, 09359, 09956 C:01305, U:01304, C:01343, G:01344
1vq4 08091 Oph·5Pout G:0918(OP1) 03631, 06732, 08125, 09411, 09867 G:02293, C:02294, C:02391, A:02465, U:0919 A:02465
1vq4 08014 Oph·Or G:02537(OP2) G:02102(O5') 03964, 04474, 07922, 09353 G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
1vq4 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03983, 04004, 04015, 07965 G:01676
1vq4 08027 Oph·Ob C:0240(OP1) G:0269(O6) 04178, 04322, 04466, 08135 G:0267, U:0268
1vq4 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03093, 04087, 07931, 09367 A:0477, A:0455, A:0460 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].


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>