MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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List of Mg2+ binding sites in structure 4qcp

4QCP (2.6Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the pre- attack state of peptide bond formation containing acylated trna- substrates in the a and p sites. this entry contains the 50s subunit of the second 70s ribosome in the asu.
List of all 94 Mg2+ binding sites in the PDB structure 4qcp 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
4qcp A3341 Ob U:A2593(O4) A4265, A4266, A4267, A4268, D409 G:A2592, C:A2591 G:A2599, G:A2592, A:A1971, A:A2600
4qcp A3347 Ob U:A2419(O4) A4280, A4281, 85101, 85102 A:A2418
4qcp A3252 Nb G:A298(N7) A4045, A4046, A4047, A4048 C:A297, G:A298, G:A338
4qcp A3464 Ob·Nb A:A1632(N7), G:A1633(O6) A4584, A4585, A4586, A4587 A:A1632, A:A1631 C:A1631, A:A1631, A:A1762
4qcp A3450 Oph G:A1997(OP2) A4544, A4545, A4546, E3101 G:A1997
4qcp A3339 Oph A:A2598(OP1) D404, D405, D406, D407, D408
4qcp A3436 Oph A:A800(OP1) A4509, A4510, A4511, A4512 C:A203, G:A799 C:A192, A:A800, A:A191
4qcp A3427 Oph G:A2035(OP1) A4486, A4487, A4488, A4489 G:A2038, G:A2037, C:A2025
4qcp A3530 Oph·Pout G:A1839(OP2) A4710, A4711, A4712, A4713 G:A1840 C:A1838 U:A1898
4qcp A3513 Oph·Pout G:A399(OP2) A4679, A4680, A4681, A4682, A4683 G:A398 G:A372, G:A400, G:A399
4qcp A3459 Oph·Pout U:A943(OP2) A4569, A4570, A4571, A4572, P306 G:A832
4qcp A3361 Oph·Pout A:A945(OP2) A4318, A4319, A4320, A4321, A4322 G:A831 G:A944 G:A944, G:A831
4qcp A3332 Oph·Pout A:A1970(OP2) A4244, A4245, A4246, A4247 A:A1900 G:A1904, G:A1835
4qcp A3566 Oph·Pout G:A1627(OP1) A4804, A4805, A4806, A4807 A:A1634
4qcp A3280 Oph·Pout C:A574(OP1) A4111, A4112, A4113, A4114, A4115 C:A2055 G:A2035, C:A531, G:A2018
4qcp A3576 Oph·Pout U:A773(OP1) A4830, A4831, A4832, A4833 G:A1356
4qcp A3321 Oph·Pout U:A588(OP2) A4207, A4208, A4209, A4210 C:A664
4qcp A3310 Oph·2Pout G:A987(OP2) A4168, A4169, A4170, 33101, 33102 A:A988, C:A986 A:A988
4qcp A3279 Oph·2Pout U:A1352(OP1) A4107, A4108, A4109, A4110 C:A1375, A:A1572 A:A1571
4qcp A3272 Oph·2Pout G:A446(OP2) A4090, A4091, A4092, A4093, A4094 C:A445, C:A1200 U:A1199 G:A446

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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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