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 4 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 A3451 Bout A4547, A4548, A4549, A4550, A4551 G:A2280 4qcp A3383 Bout A4369, A4370, A4371, A4372, A4373 G:A2000 4qcp A3590 2Bout A4866, A4867, A4868, A4869, A4870, F403 G:A798, G:A799 4qcp A3406 3Bout A4432, A4433, A4434, A4435, A4436 U:A2457, G:A2494, G:A2495 4qcp A3604 Rout·3Bout A4897, A4898, A4899, A4900, A4901, A4902 U:A395 G:A397, G:A398, G:A396 4qcp A3563 6Bout A4794, A4795, A4796, A4797, A4798, A4799 G:A2238, G:A2242, A:A2241, U:A2074, U:A2243, U:A2075 4qcp A3514 Pout·Bout A4684, A4685, A4686, A4687 G:A312 G:A301 4qcp A3549 Pout·Bout A4753, A4754, A4755, A4756, A4757 A:A1419 U:A1576 4qcp A3384 Pout·3Bout A4374, A4375, A4376, A4377, A4378, A4379 U:A1267 G:A2010, U:A2011, G:A2009 4qcp A3264 Pout·3Bout A4072, A4073, A4074, A4075, A4076 A:A299 G:A338, A:A299, A:A300 4qcp A3633 Pout·Rout·3Bout A4944, A4945, A4946, A4947 U:A1955 G:A1954 G:A1948, G:A1949, G:A1950 4qcp A3473 2Pout·Bout A4601, A4602, A4603, A4604, A4605 G:A2597, G:A1904 G:A2595 4qcp A3452 2Pout·Bout A4552, A4553, A4554, A4555 G:A770, G:A771 G:A770 4qcp A3583 2Pout·2Bout A4850, A4851, A4852, A4853, A4854, A4855 A:A1572, G:A1421 G:A1423, G:A1424 4qcp A3399 2Pout·2Bout A4412, A4413, A4414, A4415, A4416 A:A1354, A:A1353 G:A1355, G:A1356 4qcp A3340 2Pout·2Bout A4261, A4262, A4263, A4264 C:A1370, G:A1358 G:A1358, G:A1371 4qcp A3374 2Pout·4Bout A4345, A4346, A4347, A4348, A4349, A4350 C:A2452, A:A2453 A:A2453, G:A2455, A:A2497, G:A2454 4qcp A3379 2Pout·4Bout A4357, A4358, A4359, A4360, A4361 G:A2845, G:A2846 U:A2847, G:A2848, G:A2845, G:A2846 4qcp A3405 3Pout·Bout A4426, A4427, A4428, A4429, A4430, A4431 U:A2884, U:A2832, C:A2885 G:A2886 4qcp A3460 3Pout·Bout A4573, A4574, A4575, P307 G:A831, G:A944, U:A568 A:A2448

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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