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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 4qcz




4QCZ (2.8Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the pre- attack state of peptide bond formation containing short substrate- mimic cytidine-cytidine-puromycin in the a site and acylated trna in the p site. this entry contains the 50s subunit
List of all 100 Mg2+ binding sites in the PDB structure 4qcz 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 5 | « Previous | | 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
4qcz A3516 Or A:A70(O3') A4671, A4672, A4673, A4674 G:A111
4qcz A3502 Ob U:A959(O4) A4622, A4623, A4624, A4625 U:A907, A:A956, A:A957, A:A908
4qcz A3418 Ob U:A2605(O4) A4401, A4402, A4403, A4404 C:A2603, G:A2604 G:A2611, G:A2604, A:A2612
4qcz A3422 Ob U:A2431(O4) A4413, A4414, A4415, 8202 A:A2430
4qcz A3326 Nb G:A2024(N7) A4155, A4156, A4157, A4158, A4159 G:A2024 A:A2023 G:A2025
4qcz A3403 Nb G:A2054(N7) A4352, A4353, A4354, A4355, A4356 G:A2054 C:A2077, A:A2584, G:A2466, C:A2511, U:A2512, A:A2465
4qcz A3299 2Nb G:A780(N7), A:A808(N7) A4091, A4092, A4093, A4094 C:A779, G:A780, G:A807, A:A808
4qcz A3355 Oph C:A1020(OP1) A4230, A4231, A4232, A4233, A4234 G:A1019, A:A1029
4qcz A3540 Oph A:A847(OP1) A4739, A4740, A4741, A4742 G:A846 C:A181, A:A847, A:A180
4qcz A3529 Oph G:A2057(OP1) A4711, A4712, A4713, A4714 G:A2059, G:A2046
4qcz A3525 Oph A:A335(OP2) A4697, A4698, A4699, A4700 A:A334 G:A328, U:A329, G:A336, U:A327
4qcz A3357 Oph·Pout G:A832(OP2) A4236, A4237, A4238, A4239 G:A839 C:A2452 C:A2452, G:A839
4qcz A3330 Oph·Pout C:A597(OP1) A4170, A4171, A4172, A4173, A4174 C:A2077 G:A2057, G:A2040
4qcz A3408 Oph·Pout A:A1992(OP2) A4372, A4373, A4374, A4375 A:A1922 G:A1921 G:A1866
4qcz A3543 Oph·Pout A:A2717(OP2) A4747, A4748, A4749, A4750 G:A2718 A:A2717, G:A2718
4qcz A3534 Oph·Pout G:A1694(OP2) A4724, A4725, A4726, A4727 C:A1663 A:A1662 A:A1662
4qcz A3501 Oph·Pout C:A2889(OP2) A4618, A4619, A4620, A4621 U:A2888 A:A2845
4qcz A3438 Oph·Pout A:A990(OP1) A4466, A4467, A4468, A4469, A4470 G:A878 G:A879, G:A989, G:A878
4qcz A3436 Oph·Pout A:A1711(OP2) A4460, A4461, A4462, A4463, A4464 G:A2014 A:A1712, G:A1713, G:A1714, A:A1711, G:A2014
4qcz A3321 Oph·Pout G:A472(OP2) A4143, A4144, A4145, A4146 C:A471 U:A1244 G:A472

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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