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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 4qcv



4QCV (2.9Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the pre- attack state of peptide bond formation containing short substrate- mimic cytidine-puromycin in the a site and acylated trna in the p site. this entry contains the 50s subunit of the
List of all 60 Mg2+ binding sites in the PDB structure 4qcv 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 3 | « Previous | | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4qcv A3479 Ob U:A959(O4) A4550, A4551, A4552, A4553 U:A907, A:A956
4qcv A3430 Ob G:A2383(O6) A4443, A4444, A4445, A4446 G:A2382, G:A2384, G:A2357
4qcv A3396 Ob U:A2605(O4) A4368, A4369, A4370, A4371 G:A2604 G:A2604, A:A1993, A:A2612
4qcv A3401 Ob U:A2431(O4) A4381, A4382, 85101, 85102 A:A2430
4qcv A3311 Nb G:A2024(N7) A4160, A4161, A4162, A4163, A4164 G:A2024, A:A2023 G:A2025
4qcv A3382 Nb G:A2054(N7) A4328, A4329, A4330, A4331 G:A2054 C:A2077, A:A2584, G:A2466, A:A2465, C:A2511
4qcv A3280 Nb G:A322(N7) A4085, A4086, A4087, A4088 C:A321, G:A362, G:A322
4qcv A3504 Oph G:A2057(OP1) A4606, A4607, A4608, A4609, A4610 G:A2060, G:A2059, G:A2046, C:A2058
4qcv A3393 Oph A:A2610(OP1) D401, D402, D403, D404
4qcv A3385 Oph·Pout A:A1723(OP2) A4338, A4339, A4340, A4341, A4342 C:A1722 A:A1723, A:A1724
4qcv A3375 Oph·Pout G:A1232(OP2) A4303, A4304, A4305, A4306 C:A863 C:A1230 C:A864, G:A865, G:A1232
4qcv A3315 Oph·Pout C:A597(OP1) A4173, A4174, A4175, A4176, A4177 C:A2077 G:A2057, G:A2040
4qcv A3307 Oph·Pout G:A472(OP2) A4148, A4149, A4150, A4151 C:A471 U:A1244 G:A472
4qcv A3419 Oph·Pout A:A1711(OP2) A4421, A4422, A4423, A4424, A4425 G:A2014 G:A2014, A:A1712, G:A1713, G:A1714, A:A1711
4qcv A3529 Oph·Pout G:A2019(OP2) A4669, A4670, A4671, A4672 C:A2016 G:A2019
4qcv A3299 Oph·Pout G:A2361(OP1) A4133, A4134, A4135, A4136 C:A2362
4qcv A3421 Oph·Pout A:A990(OP1) A4427, A4428, A4429, A4430, A4431 G:A878 G:A879, G:A878
4qcv A3374 Oph·2Pout A:A590(OP1) A4300, A4301, A4302, P303 G:A855, G:A856 G:A856, U:A857
4qcv A3371 Oph·2Pout U:A2418(OP1) A4287, A4288, A4289, A4290 G:A2419, U:A2420 G:A2417 G:A2422
4qcv A3316 Oph·2Pout U:A2039(OP1) A4178, A4179, A4180, A4181 A:A2080, G:A2040

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].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>