`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON

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 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
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 08110 Oph·Nb U:0903(OP1) A:01357(N7) 03434, 04904, 05533, 09020 U:0904 G:0622, A:01356
1kqs 08029 cis-2Oph U:01503(OP1), C:01679(OP1) 07282, 07283, 07284, 07285 A:01504
1kqs 08018 cis-2Oph A:01291(OP1), G:01292(OP2) 03121, 06955, 07341, 09728 C:0910, U:0909 G:01292, G:0911
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 08030 cis-2Oph U:01748(OP1), U:01749(OP2) 03148, 07249, 07250, 07260 G:02585, G:02584
1kqs 08034 cis-2Oph A:02302(OP1), A:02303(OP1) 03151, 03279, 04363, 07290 A:02301, G:02304
1kqs 08048 cis-2Oph A:02746(OP2), G:02750(OP2) 05376, 05765, 07357, 07393 C:02745, U:02749
1kqs 08054 cis-2Oph C:0162(OP1), U:02276(OP1) 07253, 07304, 07305, 08946 U:0163, A:0169
1kqs 08061 cis-2Oph A:01369(OP2), U:02650(OP1) 07311, 07312, 07313, 09332 A:02649 U:01371
1kqs 08074 cis-2Oph A:01286(OP1), A:01287(OP1) 07316, 07317, 07376, V7874 A:01287
1kqs 08080 cis-2Oph A:01684(OP2), U:01724(OP2) 03710, 03988, 07328, 07380 C:01431 A:01684, A:01691, C:01692 U:01722, A:01691
1kqs 08086 cis-2Oph A:0532(OP1), U:0533(OP1) 03242, 03481, 07331, 07332 C:0534 A:02814, U:010
1kqs 08107 cis-2Oph A:01106(OP2), A:01107(OP2) 07360, 07361, 07362, 07363 C:01103, C:01104 C:01105 A:01107
1kqs 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03131, 07326, 07327, 08758 A:0882, C:0884 U:0883, A:01836
1kqs 08052 trans-2Oph U:01125(OP1), G:93092(OP1) 03132, 07372, 09103, 92357 C:01126 C:01129, G:93090
1kqs 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 03825, 07240, 07241 U:02535 U:0625 U:0626
1kqs 08079 cis-2Oph·Nb A:0167(OP1), C:0168(OP2) A:0165(N7) 03118, 03124, 03137 G:0164, A:0165 G:0164
1kqs 08089 cis-2Oph·Nb A:0516(OP1), U:0517(OP2) G:0518(N7) 07333, 07382, 07383 C:0515

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/)
For any help please contact <dust@iwonka.med.virginia.edu>