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 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 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 4qcp A3408 Oph·2Pout C:A2196(OP2) A4440, A4441, A4442, A4443 G:A2224, C:A2195 G:A2224 4qcp A3348 Oph·2Pout C:A1774(OP1) A4282, A4283, A4284, A4285, A4286 A:A1786, U:A1775 G:A1772 G:A1776, G:A1772 4qcp A3334 Oph·2Pout U:A2074(OP1) A4250, A4251, A4252, D403 G:A2239, U:A2075 G:A2238 4qcp A3320 Oph·2Pout A:A567(OP1) A4202, A4203, A4204, A4205, A4206 G:A809, G:A808 G:A809, U:A810 4qcp A3319 Oph·2Pout C:A249(OP1) A4197, A4198, A4199, A4200, A4201 G:A250, U:A2431 G:A250, C:A2394 C:A2394 4qcp A3421 Oph·2Pout G:A662(OP1) A4473, A4474, P304, P305 A:A1246, A:A1247 4qcp A3314 Oph·2Pout C:A1327(OP2) A4182, A4183, A4184, A4185, A4186 U:A1326, G:A1328 G:A1324, G:A1328 4qcp A3310 Oph·2Pout G:A987(OP2) A4168, A4169, A4170, 33101, 33102 A:A988, C:A986 A:A988 4qcp A3272 Oph·2Pout G:A446(OP2) A4090, A4091, A4092, A4093, A4094 C:A445, C:A1200 U:A1199 G:A446 4qcp A3518 Oph·2Pout A:A1938(OP2) A4691, A4692, A4693, A4694 C:A1958, C:A1957 G:A1770 4qcp A3630 Oph·2Pout G:A1187(OP2) A4937, A4938, A4939, A4940 C:A817, C:A816 G:A1187 4qcp A3261 Oph·2Pout G:A1776(OP2) A4064, A4065, A4066, A4067, A4068 A:A1981, U:A1775 G:A1776 4qcp A3279 Oph·2Pout U:A1352(OP1) A4107, A4108, A4109, A4110 C:A1375, A:A1572 A:A1571 4qcp A3282 Oph·3Pout A:A2062(OP2) A4121, A4122, A4123, A4124, A4125 G:A2444, C:A2443, G:A2061 G:A2444, G:A2445 4qcp A3579 Oph·3Pout C:A1636(OP2) A4839, A4840, A4841, A4842, A4843 U:A1300, G:A1635, A:A1637 U:A1300 4qcp A3441 Oph·3Pout G:A1828(OP2) A4526, A4527, A4528, A4529, D413 C:A1827, A:A1972, C:A1788 G:A1828 4qcp A3578 Oph·3Pout C:A2452(OP1) A4835, A4836, A4837, A4838, 0201 A:A2453, G:A2494, U:A2493 4qcp A3429 Oph·3Pout G:A1647(OP2) A4493, A4494, A4495, A4496, A4497 G:A1325, A:A1272, C:A1617 A:A1616, C:A1646 A:A1616 4qcp A3395 Oph·3Pout C:A1417(OP2) A4402, A4403, A4404, A4405 C:A1577, U:A1578, G:A1418 G:A1416 G:A1418 4qcp A3251 Oph·3Pout U:A963(OP1) A4040, A4041, A4042, A4043, A4044 C:A2498, A:A2497, G:A947

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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