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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 4dh9




4DH9 (3.2Å) -- RIBOSOME : Crystal structure of yaej bound to the 70s ribosome
List of all 19 Mg2+ binding sites in the PDB structure 4dh9 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
4dh9 A1845 Ob G:A1417(O6) A2034, A2035, A2036, A2037 G:A1415 G:A1416
4dh9 A1918 Nb G:A251(N7) A2231, A2232, A2233, A2234 A:A270, C:A271 G:A266, C:A271
4dh9 A1938 Oph C:A770(OP1) A2307, A2308, A2309, A2310
4dh9 A1878 Oph A:A937(OP2) A2103, A2104, A2105, A2106 A:A938
4dh9 A1908 Oph·Pout G:A183(OP2) A2197, A2198, A2199, A2200, A2201 U:A182
4dh9 A1933 Oph·Pout A:A608(OP2) A2287, A2288, A2289, A2290 A:A607 A:A608, A:A609
4dh9 A1955 Oph·Pout A:A1146(OP2) A2366, A2367, A2368, A2369, A2370 C:A1147 C:A1145 G:A1124, A:A1123
4dh9 A1943 Oph·2Pout A:A768(OP2) A2328, A2329, A2330, A2331 A:A767, U:A804 A:A768
4dh9 A1891 Oph·2Pout A:A860(OP2) A2132, A2133, A2134, A2135, A2136 A:A859, G:A861 G:A861
4dh9 A1936 Oph·2Pout G:A731(OP2) A2299, A2300, A2301, A2302 G:A730, C:A1527
4dh9 A1942 Oph·2Pout C:A578(OP1) A2324, A2325, A2326, A2327 G:A576, C:A817
4dh9 A1926 Oph·3Pout G:A576(OP1) A2261, A2262, A2263, A2264 G:A575, G:A577, A:A815
4dh9 A1894 4Bout A2143, A2144, A2145, A2146, A2147, A2148 G:A1419, G:A1480, U:A1481, G:A1482
4dh9 A1931 Pout·Bout A2279, A2280, A2281, A2282, A2283 U:A641 G:A595
4dh9 A1847 Pout·2Bout A2040, A2041, A2042, A2043 U:A871 G:A854, G:A853
4dh9 A1870 Pout·4Bout A2091, A2092, A2093, A2094 A:A583 G:A584, G:A585, C:A756, U:A757
4dh9 A1885 2Pout·Rout·Bout A2119, A2120, A2121, A2122, A2123 A:A915, G:A916 U:A13 G:A916
4dh9 A1884 3Pout A2117, A2118, Y317, Y318 G:A15, A:A16, U:A13
4dh9 A1886 poly-nuclear Mg2+ site A:A1500(OP1), G:A1508(OP1) G:A1504(O3') A2124, A2125, A2126 G:A1504, C:A1501, G:A1505 U:A1506

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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