MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON 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 2 of 5 | « Previous | Next » | 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 A3366 Oph·Pout A:A945(OP2) A4325, A4326, A4327, A4328, A4329 G:A831 G:A944 G:A944, G:A831 4qct A3436 Oph·2Pout G:A1647(OP2) A4505, A4506, A4507, A4508, A4509 A:A1272, G:A1325 A:A1616, C:A1646 A:A1616 4qct A3412 Oph·2Pout C:A2196(OP2) A4448, A4449, A4450, A4451 G:A2224, C:A2195 G:A2224 4qct A3353 Oph·2Pout C:A1774(OP1) A4288, A4289, A4290, A4291, A4292 U:A1775, A:A1786 G:A1772 G:A1776, G:A1772 4qct A3324 Oph·2Pout A:A567(OP1) A4203, A4204, A4205, A4206, P301 G:A809, G:A808 G:A809, U:A810 4qct A3318 Oph·2Pout C:A1327(OP2) A4182, A4183, A4184, A4185, A4186 U:A1326, G:A1328 G:A1324, G:A1328 4qct A3314 Oph·2Pout G:A987(OP2) A4167, A4168, A4169, A4170, 33101 A:A988, C:A986 A:A988 4qct A3277 Oph·2Pout G:A446(OP2) A4088, A4089, A4090, A4091, A4092 C:A445, C:A1200 U:A1199 G:A446 4qct A3265 Oph·2Pout G:A1776(OP2) A4057, A4058, A4059, A4060, A4061 A:A1981, U:A1775 G:A1776 4qct A3462 Oph·2Pout C:A574(OP2) A4569, A4570, A4571, A4572, A4573 G:A573, U:A576 G:A577, U:A576, G:A563 4qct A3535 Oph·2Pout A:A1938(OP2) A4718, A4719, A4720, A4721 C:A1957, C:A1958 4qct A3518 Oph·2Pout G:A386(OP1) A4672, A4673, A4674, A4675, A4676 G:A382, G:A381 G:A382 4qct A3266 Oph·2Pout C:A1376(OP2) A4062, A4063, A4064, A4065 U:A1352, C:A1351 G:A1377 4qct A3594 Oph·3Pout C:A2452(OP1) A4857, A4858, A4859, A4860, 0201 A:A2453, G:A2494, U:A2493 4qct A3479 Oph·3Pout G:A205(OP2) A4603, A4604, A4605, A4606, A4607 U:A202, C:A203, G:A254 C:A253 4qct A3448 Oph·3Pout G:A1828(OP2) A4538, A4539, A4540, A4541, D413 C:A1827, A:A1972, C:A1788 G:A1828 4qct A3399 Oph·3Pout C:A1417(OP2) A4408, A4409, A4410, A4411 C:A1577, U:A1578, G:A1418 G:A1416 G:A1418 4qct A3339 Oph·3Pout U:A2074(OP1) A4254, A4255, A4256, D403 G:A2239, C:A2240, U:A2075 G:A2238 4qct A3323 Oph·3Pout C:A249(OP1) A4198, A4199, A4200, A4201, A4202 G:A250, U:A2431, A:A2432 G:A250, C:A2394 A:A2393, C:A2394 4qct A3287 Oph·3Pout A:A2062(OP2) A4122, A4123, A4124, A4125, A4126 G:A2444, C:A2443, G:A2061 G:A2444, G:A2445

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].

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