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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 1k73




1K73 (3.01Å) -- RIBOSOME : Co-crystal structure of anisomycin bound to the 50s ribosomal subunit
List of all 55 Mg2+ binding sites in the PDB structure 1k73 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
1k73 A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3810, A9678 U:A2586
1k73 A8063 2Bout A4177, A7016, A7450, A7775, A7851, A7904 G:A1364, G:A1363
1k73 A8038 6Bout A3620, A3644, A3666, A3668, A7826, A9281 G:A2271, G:A2275, U:A2115, U:A2116, A:A2274, U:A2276
1k73 C8065 Pout·Rout A3966, A9924, C8521, C8551, C8603, C8634 C:A783 G:A782
1k73 D8055 2Pout A3752, A3788, A6426, A7732, A7903, D8664 U:A2721, C:A2720
1k73 A8071 2Pout·3Bout A4108, A6060, A7436, A7573, A7849, A7850 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818
1k73 48078 Mg2+ bound by non-RNA 48528, 48575, 48576 GLY:445(O), GLY:447(O), ASP:449(OD1) G:A2121, C:A2122
1k73 A8056 Mg2+ bound by non-RNA A:A2757(OP1) A3663, A3971, A7852, A9982 ASN:D335(O) A:A2719, C:A2720, G:A2758
1k73 L8069 Mg2+ bound by non-RNA A4237, A6051, L1797, L2121, L7871 ASN:L42(OD1) U:A1749, A:A2583, G:A2584, U:A2546
1k73 A8010 Mg2+ bound by non-RNA G:A836(OP1), U:A2615(OP1) A3833, A9362, D8525 GLN:D230(OE1) G:A2616
1k73 A8025 poly-nuclear Mg2+ site U:A1120(OP2), G:A1121(OP2) A4165, A7805, A7806, A7873 C:A1238 G:A1121
1k73 A8115 poly-nuclear Mg2+ site A4279, A4296, A6418, A6610, C8554, C8636 G:A1849, G:A1848
1k73 A8059 poly-nuclear Mg2+ site G:A2618(OP1) A3717, A4047, A7790, A9037, A9041 U:A2619, C:A2641, G:A2642 G:A2642, G:A2643
1k73 A8058 poly-nuclear Mg2+ site G:A2013(OP2) A3758, A7835, A7836, C8633, C8635 G:A1884, U:A1883, C:A2626
1k73 A8031 poly-nuclear Mg2+ site U:A777(OP2), C:A778(OP2) A3274, A7816, A7817, A7818

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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