MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qal:A2136, See in JSmolClick on the image to toggle views Site type: 3Pout·Rout Schematic drawing for 3Pout·Rout List of all 51 Mg2+ binding sites with the site type 3Pout·Rout 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 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 2z4k A1566 3Pout·Rout A1712, A1713, A1714, A1715, A1716, A1717 U:A854, G:A727, C:A726 C:A853 3i1o A1570 3Pout·Rout A1761, A1762, A1763, A1764, A1765 A:A523, C:A536, C:A503 C:A522 3ofx A1573 3Pout·Rout A1763, A1764, A1765, A1766, A1767, A1768 C:A504, C:A536, C:A503 C:A522 3ofa A1573 3Pout·Rout A1763, A1764, A1765, A1766, A1767, A1768 C:A504, C:A503, C:A536 C:A522 3i1m A1574 3Pout·Rout A1764, A1765, A1766, A1767, A1768, L240 C:A504, C:A536, C:A503 C:A522 3oaq A1574 3Pout·Rout A1764, A1765, A1766, A1767, A1768, A1769 C:A504, C:A503, C:A536 C:A522 3i1z A1574 3Pout·Rout A1762, A1763, A1764, A1765, A1766, L240 C:A504, C:A536, C:A503 C:A522 3i1q A1574 3Pout·Rout A1759, A1760, A1761, A1762, A1763, L240 C:A504, C:A536, C:A503 C:A522 3or9 A1574 3Pout·Rout A1763, A1764, A1765, A1766, A1767, A1768 C:A504, C:A503, C:A536 C:A522 2qbh A1589 3Pout·Rout A1823, A1824, A1825, A1826, A1827, A1828 C:A25, U:A552, A:A553 G:A524 4gas A1615 3Pout·Rout A1768, A1769, A1770, A1771, A1772, A1773 C:A536, G:A537, C:A504 C:A522 4ton A1615 3Pout·Rout A1765, A1766, A1767, A1768, A1769, A1770 C:A504, C:A503, C:A536 C:A522 4duz A1628 3Pout·Rout A1956, A1957, A1958, A1959 A:A563, U:A560, C:A562 A:A559 4gaq A1629 3Pout·Rout A1836, A1837, A1838, A1839 G:A1198, G:A1053, C:A1054 G:A1198 4gd2 A1631 3Pout·Rout A1846, A1847, A1848, A1849, N204, N205 U:A1049, G:A1048, A:A1204 C:A1203 4dr2 A1676 3Pout·Rout A2167, A2168, A2169, L302 C:A536, G:A537, A:A523 C:A522 3v26 A1721 3Pout·Rout A1994, A1995, A1996, A1997, A1998, A1999 G:A406, A:A432, A:A496 A:A495 4dv0 A1787 3Pout·Rout A2134, A2135, A2136, A2137, A2138 C:A150, A:A151, G:A168 G:A167 4duz A1810 3Pout·Rout A2102, A2103, A2104, A2105, A2106 C:A150, A:A151, G:A168 G:A167 4dv0 A1823 3Pout·Rout A2260, A2261, A2262, A2263, A2264 C:A48, U:A49, G:A115 C:A47 4dr5 A1824 3Pout·Rout A2334, A2335, A2336, A2337, A2338, A2339 C:A904, U:A891, G:A903 G:A890 4dv6 A1853 3Pout·Rout A2344, A2345, A2346, A2347, A2348 C:A328, C:A330, C:A314 A:A329 4ji7 A1976 3Pout·Rout A3360, A3361, A3362, A3363, A3364, L307 C:A536, G:A537, C:A503 C:A522 2qal A2136 3Pout·Rout A2137, A2138, A2139, A2140, A2141, A2142 U:A854, G:A727, C:A726 C:A853 1vs6 B2908 3Pout·Rout B3031, B3032, B3033, B3034, B3035, B3036 C:B560, A:B1008, G:B559 C:B1007

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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