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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 1 of 4 | « Previous | | 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 08110 Nb G:02609(N7) 03304, 03710, 03734, 05619, 05764 G:02609 U:02610, G:02606
1yjn 08084 Oph·Pout A:01742(OP2) 03647, 07831, 09253, 09378, 09757 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1yjn 08068 Oph·Pout A:02568(OP2) 03766, 04842, 06236, 07875, E920 G:02567 A:02569, A:02568
1yjn 08039 Oph·Pout U:0115(OP2) 03982, 05118, 07799, 09919 G:0112 A:0114 A:0119, G:0118
1yjn 08051 Oph·Pout G:0641(OP2) 04119, 07803, 07804 A:01355 A:01355
1yjn 08019 Oph·2Pout A:02011(OP2) 04167, 07233, 07766, 07767, 07768 A:01941, G:01891 U:01890 G:01891, C:01892
1yjn 08037 Oph·2Pout A:02553(OP2) 03143, 03217, 03661, 07850, 09077 C:02575, U:02554 C:02552 A:02576
1yjn 08020 Oph·2Pout C:01830(OP1) 07750, 07769, 09121, 09124, 09198 U:01831, A:01842 G:01828 G:01828, G:01832
1yjn 08036 Oph·3Pout G:0956(OP2) 03683, 07794, 07795, 07796, 09373 A:01006, A:0955, A:0957 A:0957, G:0956
1yjn 08040 Oph·3Pout U:0392(OP2) 03805, 04668, 07852, 07853, 09696 U:0391, C:0171, U:0172
1yjn 08017 Oph·3Pout G:0456(OP2) 03633, 03961, 07747, 09420, C8661 A:0455, G:0458, U:0457
1yjn 08032 Oph·3Pout U:02115(OP1) 03804, 04208, 09996, A8843, A8925 U:02116, G:02272, C:02273
1yjn 08021 Oph·3Pout G:02304(OP2) 03650, 03651, 07753, 07754, 09969 A:02301, A:02303, A:02305 A:02305, G:02304, U:02306
1yjn 08091 Oph·3Pout G:0918(OP1) 03330, 06489, 07835, 09092, 09550 C:02294, C:02391, A:02465 A:02465
1yjn 08035 Oph·4Pout G:01484(OP2) 03729, 07792, 07793, 07848, 07849 C:01483, C:01455, C:01456, A:01485 U:01457
1yjn 08014 Oph·Or G:02537(OP2) G:02102(O5') 03672, 04180, 07737, 09033 G:02102, G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
1yjn 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03644, 03975, 06187, 09399 G:01490, A:01487, U:01488 G:01490
1yjn 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03691, 03712, 03724, 07782 G:01676
1yjn 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03891, 04031, 04172, 07846 G:0267, U:0268
1yjn 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03798, 07746, 09048, 09785 A:0455, A:0460, A:0477 A:0455

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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