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 6 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 4nxn A1704 2Nb G:A858(N7), G:A869(N7) A2098, A2099, A2100 G:A858, C:A868, G:A869 4pe9 A1626 2Nb G:A858(N7), G:A869(N7) A1822, A1823, A1824, A1825 G:A858, C:A857, C:A868, G:A869 4pea A1625 2Nb G:A858(N7), G:A869(N7) A1816, A1817, A1818, A1819 G:A858, C:A868, G:A869 4peb A3044 2Nb G:A1358(N7), G:A1371(N7) A3404, A3405, A3406, A3407 G:A1358, G:A1371, C:A1357, C:A1370 4pec A3019 2Nb G:A733(N7), A:A761(N7) A3292, A3293, A3294, A3295 A:A761, G:A733, G:A760, C:A732 4qcn A3296 2Nb G:A780(N7), A:A808(N7) A4082, A4083, A4084, A4085 C:A779, G:A780, G:A807, A:A808 4qcr A3315 2Nb G:A780(N7), A:A808(N7) A4098, A4099, A4100, A4101 C:A779, G:A780, G:A807, A:A808 4qcz A3299 2Nb G:A780(N7), A:A808(N7) A4091, A4092, A4093, A4094 C:A779, G:A780, G:A807, A:A808 4tol A1626 2Nb G:A858(N7), G:A869(N7) A1822, A1823, A1824, A1825 G:A858, C:A868, C:A857 4tom A3044 2Nb G:A1358(N7), G:A1371(N7) A3401, A3402, A3403, A3404 G:A1358, G:A1371, C:A1357, C:A1370 4tom A3019 2Nb G:A733(N7), A:A761(N7) A3293, A3294, A3295, A3296 A:A761, G:A733, G:A760, C:A732 4ton A1625 2Nb G:A858(N7), G:A869(N7) A1817, A1818, A1819, A1820 G:A858, G:A869, C:A868 4too A3020 2Nb G:A733(N7), A:A761(N7) A3292, A3293, A3294, A3295 A:A761, G:A733, G:A760, C:A732 4tou A1626 2Nb G:A858(N7), G:A869(N7) A1822, A1823, A1824, A1825 G:A858, G:A869, C:A857, C:A868 4tov A3046 2Nb G:A1358(N7), G:A1371(N7) A3401, A3402, A3403, A3404 G:A1358, G:A1371, C:A1357, C:A1370 4tow A1625 2Nb G:A858(N7), G:A869(N7) A1816, A1817, A1818, A1819 G:A858, C:A868, G:A869 4tox A3021 2Nb G:A733(N7), A:A761(N7) A3295, A3296, A3297, A3298 A:A761, G:A733, G:A760, C:A732 4tp2 A1625 2Nb G:A858(N7), G:A869(N7) A1818, A1819, A1820, A1821 G:A858, C:A868, G:A869 4tp3 A3020 2Nb G:A733(N7), A:A761(N7) A3294, A3295, A3296, A3297 A:A761, G:A733, G:A760, C:A732 4tp4 A1625 2Nb G:A858(N7), G:A869(N7) A1821, A1822, A1823, A1824 G:A858, G:A869, C:A857, C:A868 4tp5 A3045 2Nb G:A1358(N7), G:A1371(N7) A3403, A3404, A3405, A3406 G:A1371, C:A1370 C:A1357 4tp6 A1625 2Nb G:A858(N7), G:A869(N7) A1818, A1819, A1820, A1821 G:A858, G:A869, C:A868 4tp7 A3021 2Nb G:A733(N7), A:A761(N7) A3292, A3293, A3294, A3295 A:A761, G:A733, G:A760, C:A732 4tp7 A3046 2Nb G:A1358(N7), G:A1371(N7) A3396, A3397, A3398, A3399 G:A1358, C:A1357, C:A1370 4tp8 A1626 2Nb G:A858(N7), G:A869(N7) A1821, A1822, A1823, A1824 G:A858, G:A869, C:A857, C:A868

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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