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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 1kqs



1KQS (3.1Å) -- RIBOSOME : The haloarcula marismortui 50s complexed with a pretranslocational intermediate in protein synthesis
List of all 63 Mg2+ binding sites in the PDB structure 1kqs 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
1kqs 08111 Nb G:02609(N7) 03206, 03230, 05101, 05250, 09807 G:02609 G:02606, U:02610
1kqs 08112 Nb A:0187(N1) 03236, 03277, 08647, 08844, 09080 U:0207, C:0155 G:0206 C:0438, C:0188
1kqs 08039 Oph·Pout U:0115(OP2) 03472, 04602, 07298, 07299, 09419 G:0112 A:0114 A:0119, G:0118, A:0117
1kqs 08084 Oph·Pout A:01742(OP2) 03143, 07330, 08767, 08884, 09264 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1kqs 08083 Oph·Pout A:01754(OP2) 03216, 03657, 05858, 07329, 07381 C:01753 A:01755, A:01754
1kqs 08020 Oph·2Pout C:01830(OP1) 07251, 07270, 08641, 08644, 08715 U:01831, A:01842 G:01828 G:01828, G:01832
1kqs 08092 Oph·2Pout C:01844(OP2) 03153, 03168, 07384 A:01843, A:01845 A:01845
1kqs 08068 Oph·2Pout A:02568(OP2) 03261, 04317, 05727, 07374, E920 A:02569, G:02567 A:02569, A:02568
1kqs 08072 Oph·3Pout U:0954(OP1) 03502, 06907, 07319, 07375, 09740 G:02299, A:02301, C:02298
1kqs 08037 Oph·3Pout A:02553(OP2) 03156, 07347, 08597, 09641, 09718 A:02576, U:02554, C:02575 C:02552 A:02576
1kqs 08036 Oph·3Pout G:0956(OP2) 03178, 07293, 07294, 07295, 08879 A:01006, A:0955, A:0957 A:0957, G:0956
1kqs 08032 Oph·3Pout U:02115(OP1) 03297, 03694, 09500, A8554, A8637 U:02116, G:02272, C:02273
1kqs 08035 Oph·3Pout G:01484(OP2) 03225, 07291, 07292, 07345, 07346 C:01456, A:01485, C:01455 G:01484, U:01457
1kqs 08091 Oph·3Pout G:0918(OP1) 05982, 07334, 08612, 09058, 09831 C:02294, C:02391, A:02465 A:02465
1kqs 08017 Oph·3Pout G:0456(OP2) 03130, 03452, 07248, 08928, C8470 A:0455, G:0458, U:0457
1kqs 08021 Oph·3Pout G:02304(OP2) 03146, 03147, 07254, 07255, 09473 A:02301, A:02303, A:02305 A:02305, G:02304, U:02306
1kqs 08012 Oph·4Pout G:028(OP1) 03155, 07340, 08560, 09152, 09735 C:01305, U:01304, C:01343, G:01344
1kqs 08014 Oph·Or G:02537(OP2) G:02102(O5') 03167, 03669, 07238, 08554 G:02102 C:02536, A:02101 G:02480, G:02481, A:02101
1kqs 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03141, 03466, 05676, 08906 G:01490, A:01487, U:01488 G:01489, G:01490
1kqs 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03380, 03520, 03661, L8654 G:0267, U:0268

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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