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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 3df1



3DF1 (3.5Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with hygromycin b. this file contains the 30s subunit of the first 70s ribosome, with hygromycin b bound. the entire crystal structure contains two 70s ribosomes.
List of all 55 Mg2+ binding sites in the PDB structure 3df1 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
3df1 A2025 Or C:A934(O5') A4026, A4027, A4028, A4029, A4030 C:A934, U:A1345
3df1 A2355 Ob G:A1417(O6) A4356, A4357, A4358, A4359, A4360 G:A1416, G:A1415 G:A1416, G:A1482
3df1 A2349 Ob U:A1358(O4) A4350, A4351, A4352, A4353, A4354 C:A1359, A:A1357
3df1 A2109 Ob G:A1050(O6) A4110, A4111, A4112, A4113, A4114 C:A1051, C:A1208, G:A1207
3df1 A2103 Nb G:A362(N7) A4104, A4105, A4106, A4107, A4108 G:A362, A:A364
3df1 A2187 2Nb G:A858(N7), G:A869(N7) A4188, A4189, A4190, A4191 G:A858, G:A869, C:A868
3df1 A2170 Oph A:A572(OP1) A4171, A4172, A4173, A4174, A4175
3df1 A2064 Oph A:A937(OP2) A4065, A4066, A4067, A4068, A4069 A:A938, G:A939
3df1 A2176 Oph G:A21(OP1) A4177, A4178, A4179, A4180, A4181 G:A567, A:A573
3df1 A2213 Oph·Pout A:A1433(OP2) A4214, A4215, A4216, A4217, A4218 A:A1434 A:A1434, G:A1435
3df1 A2322 Oph·Pout G:A111(OP2) A4323, A4324, A4325, A4326, A4327 C:A110 G:A112, G:A111
3df1 A2288 Oph·Pout G:A100(OP2) A4289, A4290, A4291, A4292, A4293 A:A101 C:A99 G:A100, A:A101, G:A64
3df1 A2242 Oph·Pout A:A608(OP2) A4243, A4244, A4245, A4246, A4247 A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
3df1 A2316 Oph·Pout C:A352(OP2) A4317, A4318, A4319, A4320, A4321 G:A354 G:A331, C:A330 G:A354, A:A59, C:A330
3df1 A2264 Oph·2Pout U:A1224(OP1) A4265, A4266, A4267, A4268, A4269 U:A952, G:A951 A:A977
3df1 A2306 Oph·2Pout C:A536(OP1) A4307, A4308, A4309, A4310, A4311 C:A504, G:A537
3df1 A2248 Oph·2Pout A:A1110(OP2) A4249, A4250, A4251, A4252, A4253 A:A1111, C:A1109 U:A1189, A:A1110, A:A1111
3df1 A2001 Oph·3Pout C:A578(OP1) A4002, A4003, A4004, A4005, A4006 C:A576, C:A817, U:A820 G:A575
3df1 A2164 Oph·3Pout A:A768(OP2) A4165, A4166, A4167, A4168, A4169 U:A804, C:A805, A:A767 A:A768, G:A769
3df1 A2038 Oph·4Pout A:A560(OP2) A4039, A4040, A4041, A4042, A4043 A:A563, U:A562, G:A557, G:A558 G:A566

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/)
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