MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1hr2:B15, See in JSmolClick on the image to toggle views Site type: 5Pout·Rout Schematic drawing for 5Pout·Rout List of all 12 Mg2+ binding sites with the site type 5Pout·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 1

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1hr2 B15 5Pout·Rout B356, B357, B358, B359, B360, B361 U:B202, G:B112, A:B113, C:B203, C:B128 C:B127 3ofo A1572 5Pout·Rout A1759, A1760, A1761, A1762, A1763, A1764 C:A504, G:A537, A:A523, C:A536, C:A503 C:A522 4ji1 A1795 5Pout·Rout A2462, A2463, A2464, A2465, A2466, L201 C:A536, G:A537, C:A504, A:A523, C:A503 C:A522 4ji5 A1713 5Pout·Rout A2005, A2006, A2007, A2008, A2009, L201 C:A536, G:A537, C:A504, C:A503, A:A523 C:A522 4pe9 A1640 5Pout·Rout A1881, A1882, A1883, A1884, A1885, A1886 C:A536, C:A503, G:A537, C:A504, A:A523 C:A522 4pea A1615 5Pout·Rout A1764, A1765, A1766, A1767, A1768, A1769 C:A504, A:A523, C:A536, G:A537, C:A503 C:A522 4tow A1615 5Pout·Rout A1764, A1765, A1766, A1767, A1768, A1769 C:A504, G:A537, A:A523, C:A536, C:A503 C:A522 4tp2 A1615 5Pout·Rout A1766, A1767, A1768, A1769, A1770, A1771 C:A504, G:A537, A:A523, C:A536, C:A503 C:A522 4tp8 A1640 5Pout·Rout A1881, A1882, A1883, A1884, A1885, A1886 C:A504, A:A523, C:A503, C:A536, G:A537 C:A522 4tpa A1615 5Pout·Rout A1766, A1767, A1768, A1769, A1770, A1771 C:A504, G:A537, A:A523, C:A536, C:A503 C:A522 4tpc A1640 5Pout·Rout A1881, A1882, A1883, A1884, A1885, L202 C:A504, C:A503, C:A536, G:A537, A:A523 C:A522 4tpe A1615 5Pout·Rout A1767, A1768, A1769, A1770, A1771, A1772 C:A504, G:A537, C:A503, A:A523, C:A536 C:A522

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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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