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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 4qct



4QCT (2.55Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the post-catalysis state of peptide bond formation containing dipeptydil- trna in the a site and deacylated trna in the p site. this entry contains the 50s subunit of the second 70s ribosome in
List of all 97 Mg2+ binding sites in the PDB structure 4qct 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 5 | « Previous | | 1 | 2 | 3 | 4 | 5
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4qct A3334 Ob G:A2685(O6) A4238, A4239, A4240, A4241, A4242 G:A2686, U:A2687, U:A2684
4qct A3352 Ob U:A2419(O4) A4286, A4287, 85101, 85102 A:A2418
4qct A3346 Ob U:A2593(O4) A4271, A4272, A4273, A4274, D408 G:A2592, C:A2591 G:A2599, G:A2592, A:A1971
4qct A3330 Nb G:A2032(N7) A4223, A4224, A4225, A4226 G:A2032 C:A2055, A:A2572, G:A2454, C:A2499, U:A2500, A:A2453
4qct A3255 Nb G:A298(N7) A4037, A4038, A4039, A4040 C:A297, G:A338, G:A298
4qct D303 Nb G:A1568(N7) A4982, A4983, D416, D417 G:A1568
4qct A3282 Nb G:A2002(N7) A4101, A4102, A4103, A4104, A4105 G:A2002 G:A1653, G:A2003
4qct A3472 Ob·Nb A:A1632(N7), G:A1633(O6) A4593, A4594, A4595, A4596 A:A1632, A:A1631 C:A1631, A:A1631, A:A1762
4qct A3285 Oph C:A574(OP1) A4112, A4113, A4114, A4115, A4116 G:A2035, G:A2018
4qct A3443 Oph A:A800(OP1) A4521, A4522, A4523, A4524 C:A203, G:A799 C:A192, A:A800
4qct A3344 Oph A:A2598(OP1) A4266, D404, D405, D406, D407
4qct A3336 Oph·Pout A:A1970(OP2) A4246, A4247, A4248, A4249 A:A1900 G:A1899, U:A1834 G:A1835, G:A1904
4qct A3325 Oph·Pout U:A588(OP2) A4207, A4208, A4209, A4210 C:A664
4qct A3366 Oph·Pout A:A945(OP2) A4325, A4326, A4327, A4328, A4329 G:A831 G:A944 G:A944, G:A831
4qct A3548 Oph·Pout G:A1839(OP2) A4738, A4739, A4740, A4741 G:A1840 C:A1838 U:A1898
4qct A3528 Oph·Pout G:A399(OP2) A4700, A4701, A4702, A4703, A4704 G:A398 G:A372, G:A400, G:A399
4qct A3466 Oph·Pout U:A943(OP2) A4578, A4579, A4580, P306, P307 G:A832 G:A944
4qct A3457 Oph·Pout G:A1997(OP2) A4556, E402, E403, E404 C:A1994 G:A1997
4qct A3405 Oph·Pout C:A2879(OP2) A4425, A4426, A4427, A4428, A4429 U:A2878 A:A2835
4qct A3284 Oph·Pout U:A1352(OP1) A4108, A4109, A4110, A4111 C:A1375 A:A1571

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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