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 4dr6 4DR6 (3.3Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, near-cognate transfer rna anticodon stem-loop mismatched at the first codon position and streptomycin bound List of all 48 Mg2+ binding sites in the PDB structure 4dr6 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 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 4dr6 A1602 2Bout A2003, A2004, A2005, A2006, A2007 G:A377, G:A376 4dr6 A1604 cis-2Oph C:A749(OP2), G:A750(OP2) A2011, A2012, A2013, A2014 G:A752 4dr6 A1606 trans-2Oph G:A117(OP2), G:A289(OP2) A2015, A2016, A2017, A2018 A:A116, A:A288 G:A117 4dr6 A1608 4Pout·Bout A2019, A2020, A2021, A2022 U:A751, U:A652, G:A752, C:A651 G:A752 4dr6 A1611 2Bout A2028, A2029, A2030, A2031, A2032 G:A1525, G:A1526 4dr6 A1612 3Pout·Bout A2033, A2034, A2035, A2036, A2037 C:A620, G:A617, A:A621 G:A617 4dr6 A1614 Oph A:A937(OP2) A2041, A2042, A2043, A2044 G:A939, A:A937, A:A938 4dr6 A1615 Oph G:A21(OP1) A2045, A2046, A2047 G:A568 A:A573 4dr6 A1620 Oph·Pout A:A768(OP2) A2053, A2054, A2055, A2056 C:A805 A:A768, G:A769 4dr6 A1622 Pout·3Bout A2058, A2059, A2060, A2061 A:A431 A:A408, G:A409, G:A410 4dr6 A1624 Oph A:A766(OP2) A2062, A2063, A2064, A2065 A:A767, U:A813, C:A812, C:A811 4dr6 A1626 2Bout A2066, A2067, A2068, A2069, A2070 G:A771, U:A772 4dr6 A1628 Pout A2074, A2075, A2076, A2077, A2693 G:A21 4dr6 A1633 4Pout·Rout·Bout A2085, A2086, A2087, A2088 G:A557, U:A560, C:A562, G:A558 A:A559 G:A566 4dr6 A1635 Oph·3Pout G:A588(OP2) A2094, A2095, A2096, A2097 G:A644, C:A645, C:A589 4dr6 A1640 Pout·2Bout A2104, A2105, A2106, A2107, A2108 A:A583 G:A584, G:A585 4dr6 A1641 Oph·3Pout C:A578(OP1) A2109, A2110, A2111, A2112 U:A820, G:A576, C:A817 4dr6 A1648 Bout A2123, A2124, A2125, A2126 G:A587 4dr6 A1654 2Pout A2136, A2137, A2138, A2139 G:A15, A:A16 4dr6 A1660 2Pout·3Bout A2146, A2147, A2148, A2149 A:A1110, C:A1109 C:A1189, A:A1110, A:A1111

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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