MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qou:A1560, See in JSmolClick on the image to toggle views Site type: Nb Schematic drawing for Nb List of all 284 Mg2+ binding sites with the site type Nb 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 8 of 12 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4dr6 A1688 Nb G:A362(N7) A2214, A2215, A2216, A2217 G:A361, G:A362 4duy A1672 Nb G:A362(N7) A2028, A2029, A2030, A2031 G:A361, G:A362 4duy A1679 Nb G:A324(N7) A2039, A2040, A2041, A2042 G:A326 4dv0 A1806 Nb A:A353(N7) A2199, A2200, A2201, A2202 A:A353, A:A53 4dv0 A1669 Nb G:A362(N7) A2023, A2024, A2025, A2026 G:A361 G:A361 4dv1 A1665 Nb G:A362(N7) A2022, A2023, A2024, A2025 G:A361 G:A361 4dv2 A1674 Nb G:A362(N7) A2030, A2031, A2032, A2033 G:A361, G:A362 4dv2 A1681 Nb G:A324(N7) A2041, A2042, A2043, A2044 U:A323, G:A324 4dv3 A1668 Nb G:A362(N7) A2024, A2025, A2026, A2027 G:A361, G:A362 4dv4 A1678 Nb G:A324(N7) A2031, A2032, A2033, T201 4dv5 A1665 Nb G:A362(N7) A2015, A2016, A2017, A2018 G:A361, G:A362 4dv6 A1634 Nb G:A758(N7) A1965, A1966, A1967 U:A757, G:A758 G:A581 4dv6 A1681 Nb G:A324(N7) A2035, A2036, A2037, A2038 G:A326 4dv6 A1674 Nb G:A362(N7) A2025, A2026, A2027, L302 G:A361, G:A362 G:A361 4dv6 A1834 Nb A:A353(N7) A2283, A2284, A2285, A2286 A:A53, A:A353 G:A316 4dv7 A1667 Nb G:A362(N7) A2021, A2022, A2023, A2024 G:A361, G:A362 4gaq A1610 Nb G:A324(N7) A1739, A1740, A1741, A1742, A1743 G:A326 4gaq A1612 Nb G:A362(N7) A1749, A1750, A1751, A1752, A1753 G:A361, G:A362 G:A361 4gar A3077 Nb G:A370(N7) A3560, A3561, A3562, A3563 G:A370, A:A422, A:A423 A:A270 4gas A1625 Nb G:A858(N7) A1819, A1820, A1821, A1822 G:A858, G:A869, C:A868 G:A869 4gas A1603 Nb G:A64(N7) A1706, A1707, A1708, A1709, A1710 G:A100 4gas A1609 Nb G:A324(N7) A1739, A1740, A1741, A1742, A1743 U:A323 4gas A1611 Nb G:A362(N7) A1749, A1750, A1751, A1752, A1753 4gd1 A1631 Nb G:A324(N7) A1844, A1845, A1846, A1847, A1848 G:A326 4gd1 A1603 Nb G:A362(N7) A1712, A1713, A1714, A1715, A1716 G:A362 G:A361

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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