`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 3v28



3V28 (3.1Å) -- RIBOSOME : Crystal structure of hpf bound to the 70s ribosome. this pdb entry contains coordinates for the 30s subunit with bound hpf of the 2nd ribosome in the asu
List of all 24 Mg2+ binding sites in the PDB structure 3v28 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"
Page 1 of 2 | « Previous | | 1 | 2
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v28 A1707 Ob G:A1432(O6) A1868, A1869, A1870, A1871 C:A1466
3v28 A1720 Ob G:A1417(O6) A1912, A1913, A1914, A1915 U:A1481, G:A1415, G:A1416
3v28 A1739 Nb G:A324(N7) A1976, A1977, A1978, T201, T202 U:A323
3v28 A1732 Oph G:A21(OP1) A1954, A1955, A1956, A1957 G:A567 A:A563, G:A567, A:A573
3v28 A1748 Oph A:A1360(OP1) A2004, A2005, A2006, N201 C:A1359 G:A1361, A:A1360
3v28 A1727 Oph A:A766(OP2) A1939, A1940, A1941, A1942 A:A768, C:A811, C:A812, A:A767
3v28 A1706 Oph·Pout C:A352(OP2) A1864, A1865, A1866, A1867 G:A354 C:A352, C:A330, G:A331 C:A330, A:A59
3v28 A1721 Oph·Pout U:A560(OP2) A1916, A1917, A1918, A1919 A:A563 U:A565, G:A566
3v28 A1717 Oph·Pout C:A504(OP1) A1898, A1899, A1900, A1901, A1902 C:A536 G:A505
3v28 A1731 Oph·2Pout A:A794(OP2) A1950, A1951, A1952, A1953 A:A782, C:A783 U:A1522 G:A1521
3v28 A1726 Oph·3Pout A:A768(OP2) A1935, A1936, A1937, A1938 U:A804, C:A805, A:A767 A:A768, G:A769
3v28 A1755 Oph·Ob G:A558(OP1) G:A299(O6) A2034, A2035, A2036 A:A298, G:A566
3v28 A1735 cis-2Oph C:A1054(OP2), G:A1197(OP2) A1964, A1965, A1966, A1967 G:A1053 G:A1197, G:A1198, U:A1199
3v28 A1725 Bout A1931, A1932, A1933, A1934 G:A771
3v28 A1764 2Bout A2059, A2060, A2061, A2062 G:A799, G:A800
3v28 A1765 3Bout A2063, A2064, A2065, A2066, A2067 U:A375, G:A376, G:A377
3v28 A1750 Pout A2012, A2013, A2014, A2015, A2016 G:A1421
3v28 A1754 Pout·Rout A2031, A2032, A2033, L201, L202 G:A537 C:A503
3v28 A1751 Pout·2Bout A2017, A2018, A2019, A2020, A2021, A2022 C:A398 G:A548, G:A35
3v28 A1714 Pout·3Bout A1889, A1890, A1891, A1892, A1893 A:A119 U:A287, G:A285, G:A286

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>