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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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1yhq 08041 cis-2Oph C:0162(OP1), U:02276(OP1) 08284, 08332, 08333, 09933 U:0163, A:0169
1yhq 08048 cis-2Oph A:01369(OP2), U:02650(OP1) 03322, 08339, 08340, 08341 A:02649 U:01371
1yhq 08058 cis-2Oph A:01286(OP1), A:01287(OP1) 08344, 08345, 08408, W7874 A:01287
1yhq 08062 cis-2Oph A:01684(OP2), U:01724(OP2) 04697, 04981, 08356, 08413 C:01431 A:01691, C:01692 U:01722, A:01691
1yhq 08084 cis-2Oph A:01106(OP2), A:01107(OP2) 08390, 08391, 08392, 08393 C:01103, C:01104 A:01107
1yhq 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 04117, 08303, 09504, 09522 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1yhq 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04813, 08271, 08272 U:02535 U:0625 U:0626
1yhq 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 04111, 08293, 09675 U:02484 A:02532, G:02482
1yhq 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04163, A8980, A8999
1yhq 08019 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 08308, 08309, 09894 C:02542
1yhq 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04108, 08294, 08295 G:01837 A:01839
1yhq 08006 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 04125, 08287, 08367 G:02466
1yhq A8050 Rout 04462, A8988, A9002, A9016, A9063, A9092 G:0782
1yhq 08028 6Bout 04121, 04146, 04168, 04170, 08325, 09780 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1yhq B8042 2Pout 04253, 06886, 08236, B9021, B9135, B9136 U:02721, C:02720
1yhq 08085 2Pout·Rout·2Bout 06570, 07939, 08395, 08396, 08397 U:01977, A:01978 U:01977 G:01986, G:02000
1yhq K8054 Mg2+ bound by non-RNA 03919, 04731, 06519, K2121, K7871 ASN:K42(OD1) U:02546, U:01749, A:02583, G:02584
1yhq 08043 Mg2+ bound by non-RNA A:02757(OP1) 04165, 04467, 08351, B9010 ASN:B335(O) A:02719, C:02720, G:02758
1yhq 08061 poly-nuclear Mg2+ site A:0167(OP1), C:0168(OP2) A:0165(N7) 04107, 04112, 04124 G:0164, A:0165 G:0164
1yhq 08018 poly-nuclear Mg2+ site U:01120(OP2), G:01121(OP2) 04661, 08306, 08307, 08372 C:01238 G:01121

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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