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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 4qcr



4QCR (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 first 70s ribosome in
List of all 152 Mg2+ binding sites in the PDB structure 4qcr 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 8 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4qcr A3423 Ob G:A2697(O6) A4414, A4415, A4416, A4417 G:A2698, U:A2696
4qcr A3471 Ob G:A2383(O6) A4542, A4543, A4544, A4545 G:A2382, G:A2384
4qcr A3748 Ob G:A1428(O6) A5248, A5249, A5250, A5251 G:A1426, G:A1427
4qcr A3524 Ob U:A959(O4) A4697, A4698, A4699, A4700, A4701 A:A908, U:A907, A:A956, A:A957
4qcr A3434 Ob U:A2605(O4) A4444, A4445, A4446, A4447, D406 G:A2604, C:A2603 G:A2611, G:A2604, A:A2612
4qcr A3732 Ob C:A1020(O2) A5224, A5225, A5226, A5227, A5228 A:A595, A:A1029 A:A595
4qcr A3440 Ob U:A2431(O4) A4460, A4461, 8201, 8202, 8203 A:A2430
4qcr A3419 Nb G:A2054(N7) A4395, A4396, A4397, A4398, A4399 G:A2054 G:A2466 C:A2077, A:A2584, G:A2466, C:A2511, U:A2512, A:A2465
4qcr A3383 Nb G:A2417(N7) A4278, A4279, A4280, A4281 G:A2422, G:A2417
4qcr A3342 Nb G:A2024(N7) A4169, A4170, A4171, A4172, A4173 G:A2024, A:A2023 G:A2025
4qcr A3308 Nb G:A322(N7) A4078, A4079, A4080, A4081, A4082 C:A321, G:A322, G:A362
4qcr A3596 Ob·Nb A:A1679(N7), G:A1680(O6) A4941, A4942, A4943, A4944 A:A1679, A:A1678 C:A1677, G:A1682, A:A1678, A:A1793
4qcr A3315 2Nb G:A780(N7), A:A808(N7) A4098, A4099, A4100, A4101 C:A779, G:A780, G:A807, A:A808
4qcr A3431 Oph A:A2610(OP1) A4437, D402, D403, D404, D405
4qcr A3546 Oph A:A335(OP2) A4771, A4772, A4773, A4774 A:A334 G:A328, U:A327
4qcr B210 Oph A:B25(OP1) B306, B307, B308, B309, B310 G:B24
4qcr A3673 Oph G:A426(OP2) A5098, A5099, A5100, A5101 G:A399, G:A427, G:A426
4qcr A3558 Oph A:A847(OP1) A4814, A4815, A4816, A4817, A4818 G:A846 C:A181, A:A847, A:A180
4qcr A3363 Oph·Pout A:A1018(OP2) A4235, A4236, A4237, A4238 A:A594 U:A591
4qcr A3414 Oph·Pout U:A611(OP2) A4375, A4376, A4377, A4378, A4379 C:A711

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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