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 2qow 2QOW (3.93Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin. this file contains the 30s subunit of the second 70s ribosome, with spectinomycin bound. the entire crystal structure contains two 70s ribosomes. List of all 54 Mg2+ binding sites in the PDB structure 2qow 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 2 of 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qow A1599 Oph·Ob U:A1095(OP2) G:A1108(O6) A2158, A2159, A2160, A2161 C:A1096 G:A1094 C:A1109 2qow A1566 Oph·Ob G:A558(OP1) G:A299(O6) A2001, A2002, A2003, A2004 A:A560 G:A297 A:A298, G:A566 2qow A1596 Oph·2Ob C:A980(OP2) U:A981(O4), G:A1222(O6) A2147, A2148 U:A982 G:A1221, U:A982 2qow A1545 cis-2Oph A:A509(OP2), A:A510(OP2) A1892, A1893, A1894, A1895 G:A506, C:A507 2qow A1563 cis-2Oph C:A48(OP2), G:A115(OP1) A1988, A1989, A1990, A1991 U:A49, A:A51 C:A47 2qow A1584 cis-2Oph C:A1054(OP2), A:A1197(OP2) A2088, A2089, A2090, A2091 G:A1053 G:A1198, A:A1197 2qow A1598 cis-2Oph G:A1068(OP1), G:A1094(OP1) A2154, A2155, A2156, A2157 C:A1388 2qow A1585 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A2092, A2093, A2094 2qow A1577 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2053, A2054, A2055 A:A288 G:A117, U:A118 2qow A1574 2Bout A2039, A2040, A2041, A2042, A2043, A2044 G:A38, U:A37 2qow A1559 2Bout A1966, A1967, A1968, A1969, A1970, A1971 G:A376, G:A377 2qow A1590 2Bout A2112, A2113, A2114, A2115, A2116 G:A1050, G:A1207 2qow A1592 2Bout A2126, A2127, A2128, A2129, A2130, A2131 G:A941, G:A942 2qow A1570 2Bout A2019, A2020, A2021, A2022, A2023, A2024 G:A1525, G:A1526 2qow A1582 Pout·Bout A2077, A2078, A2079, A2080, A2081, A2082 G:A1079 G:A1077 2qow A1558 Pout·Bout A1960, A1961, A1962, A1963, A1964, A1965 U:A854 G:A727 2qow A1551 Pout·2Bout A1922, A1923, A1924, A1925, A1926, A1927 A:A172 G:A147, G:A148 2qow A1580 Pout·2Bout A2066, A2067, A2068, A2069, A2070, A2071 G:A259 G:A259, G:A260 2qow A1588 Pout·2Bout A2104, A2105, A2106, A2107, A2108, A2109 A:A1046 G:A1047, G:A1048 2qow A1579 Pout·2Bout A2061, A2062, A2063, A2064, A2065 G:A111 G:A112, G:A113

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>