MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2v:B2921, See in JSmolClick on the image to toggle views Site type: 2Nb Schematic drawing for 2Nb List of all 158 Mg2+ binding sites with the site type 2Nb 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 3 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qex 08011 2Nb G:0824(N7), G:0854(N7) 03793, 04141, 04275, 04383 G:0854, U:0823, G:0824 C:0853 2qox B2941 2Nb G:B1358(N7), G:B1371(N7) B3196, B3197, B3198, B3199 C:B1357, G:B1358, G:B1371 2qox B2921 2Nb G:B733(N7), A:B761(N7) B3095, B3096, B3097, B3098 A:B761, G:B760, C:B732, G:B733 2qoy A1573 2Nb G:A858(N7), G:A869(N7) A2050, A2051, A2052, A2053 G:A858, G:A869, C:A868 2qoz B2932 2Nb G:B1358(N7), G:B1371(N7) B3642, B3643, B3644, B3645 G:B1358, G:B1371, C:B1357, C:B1370 2qoz B2959 2Nb G:B733(N7), A:B761(N7) B3766, B3767, B3768, B3769 A:B761, G:B733, G:B760, C:B732 2qp0 A1564 2Nb G:A858(N7), G:A869(N7) A1995, A1996, A1997, A1998 G:A869, G:A858, C:A868 2qp1 B2941 2Nb G:B1358(N7), G:B1371(N7) B3702, B3703, B3704, B3705 G:B1371, G:B1358, C:B1357, C:B1370 2z4k A1574 2Nb G:A858(N7), G:A869(N7) A1755, A1756, A1757, A1758 G:A858, G:A869, C:A868 2z4l B2960 2Nb G:B733(N7), A:B761(N7) B3274, B3275, B3276, B3277 A:B761, G:B760, G:B733 2z4l B2933 2Nb G:B1358(N7), G:B1371(N7) B3147, B3148, B3149, B3150 G:B1358, G:B1371, C:B1357, C:B1370 2z4m A1577 2Nb G:A858(N7), G:A869(N7) A1775, A1776, A1777, A1778 G:A869, G:A858, C:A868, C:A857 2z4n B2942 2Nb G:B1358(N7), G:B1371(N7) B3198, B3199, B3200, B3201 G:B1371, G:B1358, C:B1357, C:B1370 2z4n B2922 2Nb G:B733(N7), A:B761(N7) B3097, B3098, B3099, B3100 G:B733, G:B760, A:B761 C:B732 3cc2 08011 2Nb G:0824(N7), G:0854(N7) 03514, 03852, 03986, 04093 G:0854, G:0824, U:0823, C:0853 3cxc 08011 2Nb G:0824(N7), G:0854(N7) 04906, 05231, 05359, 05460 G:0854, U:0823, G:0824, C:0853 3df1 A2187 2Nb G:A858(N7), G:A869(N7) A4188, A4189, A4190, A4191 G:A858, G:A869, C:A868 3df2 B3164 2Nb G:B1358(N7), G:B1371(N7) B4165, B4166, B4167, B4168 G:B1358, G:B1371, C:B1357, C:B1370 3df2 B3321 2Nb G:B733(N7), A:B761(N7) B4322, B4323, B4324, B4325 A:B761, C:B732, G:B733 G:B760 3df4 B3220 2Nb G:B1358(N7), G:B1371(N7) B4221, B4222, B4223, B4224 G:B1371, G:B1358, C:B1357, C:B1370 3df4 B3099 2Nb G:B733(N7), A:B761(N7) B4100, B4101, B4102, B4103 A:B761, G:B760, C:B732, G:B733 3i1m A1559 2Nb G:A858(N7), G:A869(N7) A1699, A1700, A1701, A1702 G:A858, G:A869, C:A868 3i1n A2923 2Nb G:A733(N7), A:A761(N7) A3137, A3138, A3139, A3140 G:A733, A:A761 C:A732 3i1o A1556 2Nb G:A858(N7), G:A869(N7) A1698, A1699, A1700, A1701 G:A858, C:A868, G:A869 3i1p A2924 2Nb G:A733(N7), A:A761(N7) A3144, A3145, A3146, A3147 A:A761, G:A733, G:A760, C:A732

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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