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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 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03123, 07262, 08694 U:02484 A:02532, G:02482
1kqs 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 03825, 07240, 07241 U:02535 U:0625 U:0626
1kqs 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03174, 08543, A8537
1kqs 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03291, 07247, 08568, 09290 A:0455, A:0460, A:0477 A:0455
1kqs 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03119, 07263, 07264 G:01837 A:01839
1kqs 08006 poly-nuclear Mg2+ site U:0821(OP2), C:0822(OP2), G:0854(OP1) 03125, 03263, 09322 G:0856, U:0855
1kqs 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 07252, 08529, 09866 G:0833
1kqs 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03138, 07256, 07339 G:02466, C:0920
1kqs 08009 poly-nuclear Mg2+ site G:02611(OP1), A:02612(OP1) 03249, 06920, 07257, 07258 G:02094, G:02093
1kqs 08010 Mg2+ bound by non-RNA G:0836(OP1), U:02615(OP1) 03347, 08873, B8524 GLN:B230(OE1) G:02616
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 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 03256, 07265, 07266
1kqs 08017 Oph·3Pout G:0456(OP2) 03130, 03452, 07248, 08928, C8470 A:0455, G:0458, U:0457
1kqs 08018 cis-2Oph A:01291(OP1), G:01292(OP2) 03121, 06955, 07341, 09728 C:0910, U:0909 G:01292, G:0911
1kqs 08020 Oph·2Pout C:01830(OP1) 07251, 07270, 08641, 08644, 08715 U:01831, A:01842 G:01828 G:01828, G:01832
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 08022 cis-2Oph G:02097(OP2), G:02540(OP1) 03377, 07259, 08629, 08971 A:02095 A:02096 G:02097
1kqs 08023 cis-2Oph G:02617(OP2), G:02618(OP2) 03136, 03329, 07275, 07276 G:02616 G:02618, U:02619
1kqs 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07278, 07279, 08903 C:02542

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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