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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 4nvx




4NVX (3Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of antibiotic dityromycin bound to 70s ribosome
List of all 56 Mg2+ binding sites in the PDB structure 4nvx 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
4nvx A3322 Ob U:A2593(O4) A4222, A4223, A4224, A4225, D405 C:A2591, G:A2592 G:A2592, A:A1971
4nvx A3262 Nb G:A2002(N7) A4081, A4082, A4083, A4084, A4085 G:A2002 G:A1653, G:A2003, G:A2004
4nvx A3624 Nb G:A2502(N7) A4850, A4851, A4852, A4853 G:A2446, G:A2447, G:A2502
4nvx A3399 Oph G:A2035(OP1) A4402, A4403, A4404, A4405 G:A2024, G:A2038, C:A2025, G:A2037
4nvx A3491 Oph G:A399(OP2) A4576, A4577, A4578, A4579 G:A400
4nvx A3265 Oph C:A574(OP1) A4090, A4091, A4092, A4093 G:A2035
4nvx A3630 Oph G:A1997(OP2) A4863, A4864, E402, E403
4nvx A3320 Oph A:A2598(OP1) A4217, D401, D402, D403, D404
4nvx A3314 Oph·Pout A:A1970(OP2) A4203, A4204, A4205, A4206 A:A1900 G:A1899, U:A1834 G:A1835
4nvx A3428 Oph·Pout U:A943(OP2) A4465, A4466, A4467, P304, P305 G:A832 G:A944
4nvx A3392 Oph·Pout U:A2022(OP1) A4382, A4383, A4384, A4385 G:A2023 G:A530
4nvx A3302 Oph·Pout A:A567(OP1) A4169, A4170, A4171, A4172 G:A808 G:A809, U:A810
4nvx A3341 Oph·Pout A:A945(OP2) A4264, A4265, A4266, A4267, A4268 G:A831 G:A944 G:A944, G:A831
4nvx A3424 Oph·2Pout C:A574(OP2) A4457, A4458, A4459, A4460, A4461 G:A573, U:A576 G:A577
4nvx A3347 Oph·2Pout U:A1313(OP1) A4278, A4279, A4280, A4281 C:A1333, G:A1334
4nvx A3606 Oph·2Pout U:A2492(OP1) A4800, A4801, A4802, A4803 G:A2454, A:A2453 C:A2573 C:A2573
4nvx A3510 Oph·2Pout G:A1839(OP2) A4607, A4608, A4609, A4610 G:A1897, G:A1840 C:A1838 G:A1897, U:A1898
4nvx A3315 Oph·2Pout A:A1970(OP1) A4207, A4208, A4209, A4210 A:A1971, A:A1969
4nvx A3412 Oph·3Pout G:A1828(OP1) A4431, A4432, A4433, A4434 A:A1972, A:A1773, G:A1973
4nvx A3301 Oph·3Pout C:A249(OP1) A4164, A4165, A4166, A4167, A4168 G:A250, U:A2431, A:A2432 G:A250, C:A2394 C:A2394

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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