MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vqo:08005, See in JSmolClick on the image to toggle views Site type: mer-3Oph Schematic drawing for mer-3Oph List of all 430 Mg2+ binding sites with the site type mer-3Oph 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 18 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1hr2 A3 mer-3Oph A:A184(OP1), A:A186(OP1), A:A187(OP2) A325, A326, A327 A:A183, G:A188 1hr2 B4 mer-3Oph A:B184(OP1), A:B186(OP1), A:B187(OP2) B329, B330, B331 A:B183, G:B188 3owi A104 mer-3Oph C:A74(OP1), A:A75(OP1), A:A76(OP2) A143, A144, A145 A:A76, A:A77 3owz A104 mer-3Oph C:A74(OP1), A:A75(OP1), A:A76(OP2) A132, A133, A134 A:A77, A:A76 3oxm B110 mer-3Oph C:B74(OP1), A:B75(OP1), A:B76(OP2) B106, B107, B116 A:B77, A:B76 3oxd B114 mer-3Oph C:B74(OP1), A:B75(OP1), A:B76(OP2) B146, B147, B148 A:B77, A:B78, A:B76 3oww B122 mer-3Oph C:B74(OP1), A:B75(OP1), A:B76(OP2) B167, B168, B169 A:B76, A:B77, A:B78 3b4a B201 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A301, A302, B303 G:A3 G:A1, A:B35 2ho6 B201 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A302, A303, B304 A:B35, G:A1 2z75 B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A401, B402, B465 G:A1, A:B35 2h0s B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A229, B220, B230 G:A1, A:B35 3b4c B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B402, A401 G:A1, A:B35 3b4b B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B403, B404, B405 G:A1 2gcv B401 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B282, B324, B325 G:A1, A:B35 2h0w B501 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A282, A324, B325 G:A1, A:B35 2gcs B501 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B261, B288, B289 G:A1, A:B35 2h0x B501 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B261, B288, B289 G:A1, A:B35 3r1l F1021 mer-3Oph C:F70(OP1), G:F72(OP2), U:F106(OP1) F1048, F1049, F1050 A:F71 3r1l C1021 mer-3Oph C:C70(OP1), G:C72(OP2), U:C106(OP1) C1052, C1053, C1054 A:C71 3i1s A1538 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1608, A1609, A1610 U:A571 3i1o A1538 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1608, A1609, A1610 3ora A1541 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1613, A1614, A1615 U:A571 3oar A1541 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1608, A1609, A1610 3ofb A1541 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1609, A1610, A1611 2qbf A1544 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1609, A1610, A1611 U:A571 A:A574

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>