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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 1yjn



1YJN (3Å) -- RIBOSOME : Crystal structure of clindamycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
List of all 63 Mg2+ binding sites in the PDB structure 1yjn 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 2 of 4 | | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1yjn 08109 Oph·Nb U:0903(OP1) A:01357(N7) 03943, 05415, 06048, 09513 U:0904 G:0622, A:01356
1yjn 08022 cis-2Oph G:02097(OP2), G:02540(OP1) 03888, 07758, 09109, 09462 A:02095 A:02096 G:02097
1yjn 08009 cis-2Oph G:02611(OP1), A:02612(OP1) 03752, 07423, 07756, 07757 G:02094, G:02093
1yjn 08013 cis-2Oph G:0877(OP1), G:02623(OP1) 03654, 03667, 07770, 09019 C:02475, A:02624 G:0885
1yjn 08018 cis-2Oph A:01291(OP1), G:01292(OP2) 03226, 03624, 07458, 07842 C:0910, U:0909 G:0911, G:01292
1yjn 08023 cis-2Oph G:02617(OP2), G:02618(OP2) 03639, 03838, 07774, 07775 G:02616 G:02618
1yjn 08025 cis-2Oph U:01120(OP2), G:01121(OP2) 04186, 07776, 07777, 07845 C:01238 G:01121
1yjn 08029 cis-2Oph U:01503(OP1), C:01679(OP1) 07783, 07784, 07785, 07786 A:01504
1yjn 08030 cis-2Oph U:01748(OP1), U:01749(OP2) 03652, 07748, 07749, 07759 G:02585, G:02584
1yjn 08031 cis-2Oph U:0777(OP2), C:0778(OP2) 03281, 07788, 07789, 07790
1yjn 08034 cis-2Oph A:02302(OP1), A:02303(OP1) 03655, 03785, 04886 A:02301, G:02304
1yjn 08052 cis-2Oph U:01125(OP1), G:992(OP1) 03635, 03875, 98589, 98721 C:01126 C:01129, G:990
1yjn 08054 cis-2Oph C:0162(OP1), U:02276(OP1) 07752, 07805, 07806, 09437 U:0163, A:0169
1yjn 08061 cis-2Oph A:01369(OP2), U:02650(OP1) 07812, 07813, 07814, 09826 A:02649 U:01371
1yjn 08074 cis-2Oph A:01286(OP1), A:01287(OP1) 07817, 07818, 07876, W7874 A:01287
1yjn 08080 cis-2Oph A:01684(OP2), U:01724(OP2) 04224, 04516, 07829, 07879 C:01431 A:01684, C:01692 U:01722, A:01691
1yjn 08089 cis-2Oph A:0516(OP1), U:0517(OP2) 07834, 07881, 07882 C:0515 G:0518
1yjn 08106 cis-2Oph A:01106(OP2), A:01107(OP2) 07862, 07863, 07864, 07865 C:01103, C:01104 A:01107
1yjn 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03634, 07827, 07828, 09244 A:0882, C:0884 U:0883, A:01836
1yjn 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04345, 07739, 07740 U:02535 U:0625 U:0626

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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