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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 4nvz




4NVZ (3.1Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of antibiotic ge82832 bound to 70s ribosome
List of all 72 Mg2+ binding sites in the PDB structure 4nvz 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
4nvz A3422 Ob G:A2697(O6) A4398, A4399, A4400, A4401 A:A2734 G:A2698, U:A2696
4nvz A3483 Ob C:A1020(O2) A4549, A4550, A4551, A4552 A:A595
4nvz A3518 Ob U:A959(O4) A4631, A4632, A4633, A4634, A4635 A:A908, U:A907, A:A956, A:A957
4nvz A3438 Ob U:A2431(O4) A4436, A4437, A4438, 8201, 8202
4nvz A3343 Nb G:A2024(N7) A4179, A4180, A4181, A4182, A4183 G:A2024 G:A2025, G:A2026
4nvz A3304 Nb G:A322(N7) A4078, A4079, A4080, A4081, A4082 G:A322
4nvz A3431 Oph A:A2610(OP1) D402, D403, D404, D405, D406
4nvz A3546 Oph G:A2057(OP1) A4707, A4708, A4709, A4710 G:A2059, C:A2047
4nvz A3578 Oph·Pout C:A597(OP2) A4790, A4791, A4792, A4793 G:A596 U:A599, G:A600
4nvz A3584 Oph·Pout U:A988(OP2) A4804, A4805, A4806, P305, P306 G:A879
4nvz A3345 Oph·Pout U:A1398(OP1) A4187, A4188, A4189, A4190, A4191 C:A1421 A:A1618
4nvz A3453 Oph·Pout A:A1711(OP2) A4482, A4483, A4484, A4485, A4486 G:A2014 G:A2014, A:A1712, G:A1713, G:A1714, A:A1711
4nvz A3421 Oph·Pout A:A1723(OP2) A4393, A4394, A4395, A4396, A4397 C:A1722 G:A1721 A:A1723, A:A1724
4nvz B3011 Oph·Pout G:B101(OP2) B4012, B4013, B4014, B4015 A:B102 A:B102
4nvz A3409 Oph·2Pout A:A590(OP1) A4347, A4348, A4349, A4350, A4351 G:A855, G:A856 G:A856, U:A857
4nvz A3408 Oph·2Pout C:A238(OP1) A4342, A4343, A4344, A4345, A4346 U:A2443, A:A2444 G:A239, C:A2406 C:A2406
4nvz A3363 Oph·2Pout G:A1254(OP2) A4237, A4238, A4239, A4240 C:A337, A:A1255 A:A355
4nvz A3338 Oph·2Pout G:A472(OP2) A4164, A4165, A4166, A4167, A4168 C:A471, C:A1245
4nvz A3330 Oph·2Pout G:A848(OP2) A4148, A4149, A4150, A4151, F401 G:A845, G:A846
4nvz A3320 Oph·2Pout G:A1807(OP2) A4123, A4124, A4125, A4126, A4127 A:A2003, U:A1806 G:A1807

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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