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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 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 3 of 5 | | | 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 A3440 Oph·4Pout G:A1828(OP1) A4521, A4522, A4523, A4524, A4525 G:A1772, A:A1972, A:A1773, G:A1973
4qcp A3281 Oph·4Pout U:A2017(OP1) A4116, A4117, A4118, A4119, A4120 A:A578, G:A577, A:A2058, G:A2018
4qcp A3328 Oph·4Pout G:A741(OP1) A4229, A4230, A4231, A4232 A:A1784, A:A1785, G:A2608, C:A1983 G:A2607
4qcp A3327 Oph·Ob A:A2033(OP1) U:A2028(O4) A4225, A4226, A4227, A4228 G:A2029, G:A2027
4qcp A3353 Oph·Ob C:A2248(OP2) U:A2249(O4) A4295, A4296, A4297, A4298 A:A2247, C:A2066, G:A2253
4qcp A3620 Oph·Ob C:A453(OP1) G:A450(O6) A4923, A4924, A4925, A4926 A:A449, A:A454 A:A449
4qcp A3357 cis-2Oph U:A1394(OP1), C:A1604(OP1) A4306, A4307, A4308, A4309 A:A1395
4qcp A3311 cis-2Oph G:A2056(OP2), A:A2057(OP2) A4171, A4172, A4173, A4174 A:A2503, U:A2504, G:A2505 A:A2503 A:A2058, A:A2057
4qcp A3318 cis-2Oph U:A2431(OP2), A:A2432(OP2) A4193, A4194, A4195, A4196 A:A2433
4qcp A3345 cis-2Oph A:A2711(OP1), A:A2712(OP1) A4275, A4276, A4277, A4278 C:A1297
4qcp A3394 cis-2Oph G:A2061(OP2), G:A2502(OP2) A4398, A4399, A4400, A4401 G:A2446 C:A2501, A:A2060 G:A2445, G:A2446, A:A2060
4qcp A3412 cis-2Oph A:A784(OP1), G:A2588(OP1) A4450, A4451, A4452, D412 C:A2440, A:A2589 G:A792
4qcp A3419 cis-2Oph A:A804(OP1), G:A805(OP1) A4470, P301, P302, P303
4qcp A3461 cis-2Oph A:A945(OP2), G:A946(OP2) A4576, A4577, A4578, A4579 U:A822 G:A944
4qcp A3553 cis-2Oph C:A192(OP1), U:A2243(OP1) A4771, A4772, A4773, A4774 A:A199
4qcp A3569 cis-2Oph A:A1269(OP2), A:A2005(OP1) A4811, A4812, A4813, A4814 A:A1268, C:A2006 A:A1269
4qcp A3323 trans-2Oph A:A751(OP1), A:A1614(OP1) A4215, A4216, A4217, A4218 G:A1613 A:A751, C:A1617, A:A789, A:A1614, C:A1615
4qcp A3344 trans-2Oph C:A1298(OP2), U:A1639(OP2) A4271, A4272, A4273, A4274 C:A1297, C:A1638 C:A2710 G:A1299
4qcp A3322 trans-2Oph U:A787(OP1), C:A790(OP2) A4211, A4212, A4213, A4214 C:A791, A:A789 A:A1780
4qcp A3171 fac-3Oph·Ob A:A1669(OP2), C:A1670(OP2), G:A2550(OP1) U:A1671(O4)

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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