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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 2qoz:B2982, See in JSmolMgRNA representative site for type PO-3BO         Click on the image to toggle views


Site type: Pout·3Bout

Schematic drawing for
Pout·3Bout

MgRNA type PO-3BO
List of all 341 Mg2+ binding sites with the site type Pout·3Bout in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
Page 3 of 14 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qbd A2084 Pout·3Bout A2085, A2088, A2089, A2090, N2086, N2087 A:A1360 C:A980, G:A1361, A:A1360
2qbd A2122 Pout·3Bout A2123, A2124, A2125, A2126, A2127, A2128 A:A781 U:A798, G:A799, G:A800
2qbd A2115 Pout·3Bout A2116, A2117, A2118, A2119, A2120, A2121 G:A266 G:A257, G:A258, G:A259
2qbe B3450 Pout·3Bout B3976, B3977, B3978, B3979, B3980, B3981 A:B2386 C:B2326, A:B2386, U:B2387
2qbf A1567 Pout·3Bout A1722, A1723, A1724, A1725, A1726, A1727 A:A781 G:A800, U:A798, G:A799
2qbf A1562 Pout·3Bout A1693, A1694, A1695, A1696, A1697, A1698 U:A644 G:A645, G:A592, G:A646
2qbg B2957 Pout·3Bout B3270, B3271, B3272, B3273, B3274, B3275 A:B2386 C:B2326, A:B2386, U:B2387
2qbh A1563 Pout·3Bout A1699, A1700, A1701, A1702, A1703, A1704 A:A781 G:A800, G:A799, U:A798
2qbh A1599 Pout·3Bout A1871, A1872, A1873, A1874, A1875, A1876 C:A1400 C:A1399, G:A926, G:A1505
2qbh A1562 Pout·3Bout A1693, A1694, A1695, A1696, A1697, A1698 G:A266 G:A257, G:A258, G:A259
2qbj A1567 Pout·3Bout A1722, A1723, A1724, A1725, A1726, A1727 A:A781 G:A800, U:A798, G:A799
2qbk B2957 Pout·3Bout B3266, B3267, B3268, B3269, B3270, B3271 A:B2386 C:B2326, A:B2386, U:B2387
2qbk B2927 Pout·3Bout B3125, B3126, B3127, B3128, B3129, B3130 A:B616 G:B618, G:B619, G:B617
2qbk B2917 Pout·3Bout B3077, B3078, B3079, B3080, B3081, B3082 A:B2033 G:B2027, U:B2028, G:B2029
2qou A1557 Pout·3Bout A1964, A1965, A1966, A1967, A1968, A1969 A:A1360 C:A980, A:A1360, C:A979
2qou A1562 Pout·3Bout A1990, A1991, A1992, A1993, A1994, A1995 G:A266 G:A257, G:A258, U:A268
2qou A1545 Pout·3Bout A1908, A1909, A1910, A1911, A1912, A1913 G:A803 U:A772, G:A773, G:A771
2qou A1574 Pout·3Bout A2052, A2053, A2054, A2055, A2056, A2057 G:A1385 G:A1385, G:A1386, C:A1384
2qov B2924 Pout·3Bout B3109, B3110, B3111, B3112, B3113, B3114 A:B756 A:B756, A:B739, G:B757
2qov B2982 Pout·3Bout B3382, B3383, B3384, B3385, B3386, B3387 A:B2386 C:B2326, A:B2386, U:B2387
2qow A1556 Pout·3Bout A1948, A1949, A1950, A1951, A1952, A1953 G:A266 G:A259, G:A257, G:A258
2qow A1557 Pout·3Bout A1954, A1955, A1956, A1957, A1958, A1959 A:A781 G:A800, U:A798, G:A799
2qow A1554 Pout·3Bout A1936, A1937, A1938, A1939, A1940, A1941 U:A644 G:A592, G:A646, G:A645
2qow A1589 Pout·3Bout A2110, A2111, N280, N281, N1823, N1826 A:A1360 C:A980, G:A1361, A:A1360
2qox B2917 Pout·3Bout B3075, B3076, B3077, B3078, B3079, B3080 A:B2033 G:B2027, U:B2028, G:B2029

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>