MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3r8s:A2930, See in JSmolClick on the image to toggle views Site type: Oph Schematic drawing for Oph List of all 588 Mg2+ binding sites with the site type Oph 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 24 | « 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 3la5 A1 Oph A:A24(OP1) A105, A108, A109, A113, A120 G:A72, A:A24 3jxq L7 Oph G:L6(OP2) L112, L116, L122, L123 C:B1 6tna A77 Oph G:A19(OP1) A145, A146, A147, A148, A149 G:A20, U:A59, C:A60, C:A56 4tra A77 Oph G:A19(OP1) A185, A186, A187, A188, A189 G:A20 1tra A79 Oph G:A19(OP1) A175, A176, A177, A178, A179 G:A20, U:A59, C:A60 4enc A102 Oph A:A40(OP2) A201, A209, A210, A211 A:A40 A:A49, U:A7, C:A50 1y26 X102 Oph A:X24(OP1) X273, X274, X275, X276, X277 G:X72, A:X24 4tzx X103 Oph A:X24(OP1) X242, X246, X251, X272, X302 G:X72, A:X24 1y26 X105 Oph A:X23(OP2) X290, X291, X292, X293, X294 U:X22 A:X21 4ena A111 Oph A:A40(OP2) A202, A203, A204, A205 A:A40 U:A7, C:A50 4jf2 A120 Oph A:A10(OP1) A331, A332, A333, A334, A335 A:A10 3i20 B123 Oph G:B100(OP2) B661, B662, B663, B664, B665 A:B73 A:B101, G:B102 4tpf B201 Oph A:B58(OP2) B301, B302, B303, B304 G:B56 A:B58, A:B59, U:B22, G:B23 4too B201 Oph A:B58(OP2) B301, B302, B303, B304 G:B56 A:B58, A:B59, U:B22, G:B23 4tp7 B201 Oph A:B58(OP2) B301, B302, B303, B304 G:B56, A:B57 A:B58, U:B22, G:B23 4qcr B210 Oph A:B25(OP1) B306, B307, B308, B309, B310 G:B24 1yls B240 Oph U:B234(OP1) B345, B346, B347, B348, B349 G:B236, G:B237 1yls D340 Oph U:D234(OP1) D389, D390, D391, D392, D393 G:D236, G:D237 4lx5 A503 Oph A:A24(OP1) A604, A610, A611, A612, A613 A:A24, G:A72 3mxh R670 Oph A:R48(OP2) R729, R730, R731, R732, R733 A:R47 G:R14, A:R91 3mum R670 Oph A:R48(OP2) R706, R707, R708, R709, R710 A:R47 A:R91, G:R14 1evv A903 Oph G:A19(OP1) A918, A919, A920, A921, A922 G:A20, U:A59, C:A60, C:A56 3i1s A1544 Oph C:A934(OP1) A1637, A1638, A1639, A1640, A1641 3i1o A1544 Oph C:A934(OP1) A1637, A1638, A1639, A1640, A1641 3i21 A1544 Oph C:A934(OP1) A1637, A1638, A1639, A1640, A1641

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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