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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 1q81



1Q81 (2.95Å) -- RIBOSOME : Crystal structure of minihelix with 3' puromycin bound to a- site of the 50s ribosomal subunit.
List of all 58 Mg2+ binding sites in the PDB structure 1q81 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
1q81 A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3127, A7260, A8699 U:A2484 A:A2532, G:A2482
1q81 A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3179, A8542, C8539
1q81 A8006 fac-3Oph U:A821(OP2), C:A822(OP2), G:A854(OP1) A3129, A3267, A9326 G:A856, U:A855
1q81 A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3259, A7263, A7264
1q81 A8026 fac-3Oph C:A2608(OP1), G:A2609(OP1), U:A2610(OP2) A7276, A7277, A8904
1q81 A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A7250, A8528, A9870 G:A833
1q81 A8005 mer-3Oph A:A1836(OP1), U:A1838(OP1), A:A1839(OP2) A3123, A7261, A7262 G:A1837 A:A1839
1q81 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3142, A7254, A7338 G:A2466
1q81 A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A3609, A9123
1q81 A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3330, A9190
1q81 C8065 Rout A3482, A9441, C8521, C8558, C8616, C8643 G:A782
1q81 A8063 2Bout A3691, A6500, A6926, A7244, A7321, A7373 G:A1364, G:A1363
1q81 A8038 6Bout A3138, A3162, A3184, A3186, A7295, A8799 G:A2271, G:A2275, U:A2115, U:A2116, A:A2274, U:A2276
1q81 A8071 2Pout·3Bout A3622, A5569, A6910, A7049, A7319, A7320 A:A1815, C:A1816 U:A1813, C:A1818, U:A1817
1q81 A8010 Mg2+ bound by non-RNA G:A836(OP1), U:A2615(OP1) A3354, A8876, D8529 GLN:D230(OE1) G:A2616
1q81 A8056 Mg2+ bound by non-RNA A:A2757(OP1) A3181, A3486, A7322, D8545 ASN:D335(O) A:A2719, C:A2720, G:A2758
1q81 A8096 poly-nuclear Mg2+ site G:A1848(O6), G:A1849(O6) A3176, A3213, A3348 A:A1847 U:A1883, G:A1884
1q81 A8058 poly-nuclear Mg2+ site G:A2013(OP2) A3276, A7305, A7306, C8642, C8644 G:A1884, U:A1883, C:A2626

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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