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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 1yhq



1YHQ (2.4Å) -- RIBOSOME : Crystal structure of azithromycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
List of all 45 Mg2+ binding sites in the PDB structure 1yhq 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
1yhq 08088 Nb A:0187(N1) 03071, 04222, 04263, 09626, 09828 C:0155, U:0207 G:0206 C:0188, C:0438
1yhq 08029 Oph·Pout U:0115(OP2) 03413, 04458, 05579, 08326, 08327 G:0112 A:0114 G:0118, A:0119
1yhq 08065 Oph·Pout A:01742(OP2) 03254, 04130, 08358, 09749, 09873 G:02033 G:02033, G:01744, G:01745, A:01742, G:01743
1yhq 08064 Oph·2Pout A:01754(OP2) 04204, 04644, 06828, 08357, 08414 C:01753, A:01755 A:01755, A:01754
1yhq 08013 Oph·2Pout A:02011(OP2) 04643, 07691, 08298, 08299, 08300 A:01941, G:01891 U:01890 G:01891, C:01892
1yhq 08026 Oph·2Pout G:0956(OP2) 04167, 08321, 08322, 08323, 09866 A:01006, A:0955 A:0957, G:0956
1yhq 08014 Oph·2Pout C:01830(OP1) 08282, 08301, 09619, 09622, 09696 U:01831, A:01842 G:01828 G:01828, G:01832
1yhq 08015 Oph·3Pout G:02304(OP2) 03467, 04134, 04135, 08285, 08286 A:02301, A:02305, A:02303 U:02306, A:02305, G:02304
1yhq 08012 Oph·3Pout G:0456(OP2) 04435, 07845, 08279, 09915, C8562 G:0458, A:0455, U:0457
1yhq 08025 Oph·3Pout U:02115(OP1) 03492, 04284, 04682, A9015, A9090 G:02272, C:02273, U:02116
1yhq 08008 Oph·4Pout G:028(OP1) 03139, 03729, 04144, 08368, 09537 C:01343, G:01344, C:01305, U:01304
1yhq 08070 Oph·4Pout G:0918(OP1) 03049, 03824, 06950, 08362, 09588 A:02465, G:02293, C:02294, C:02391 A:02465
1yhq 08020 Oph·Ob C:0240(OP1) G:0269(O6) 04367, 04508, 04648, 08373 G:0267, U:0268
1yhq 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03279, 04278, 08278, 09545 A:0477, A:0455, A:0460 A:0455
1yhq 08021 Oph·Ob A:01448(OP2) U:01677(O4) 04175, 04196, 04207, S8993 G:01676
1yhq 08087 Oph·Nb U:0903(OP1) A:01357(N7) 03010, 04418, 05880, 06508 U:0904 A:01356, G:0622
1yhq 08023 cis-2Oph U:01748(OP1), U:01749(OP2) 04136, 08280, 08281, 08291 G:02585, G:02584
1yhq 08016 cis-2Oph G:02097(OP2), G:02540(OP1) 04364, 08290, 09607, 09957 A:02095 A:02096 G:02097
1yhq 08010 cis-2Oph G:02102(OP2), G:02537(OP2) 04156, 04656, 08269, 09531 G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
1yhq 08009 cis-2Oph G:0877(OP1), G:02623(OP1) 04138, 04151, 09519, A9089 C:02475, A:02624 G:0885

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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