MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·2Bout Schematic drawing for 2Pout·2Bout List of all 279 Mg2+ binding sites with the site type 2Pout·2Bout 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 12 | « 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 2z4m A1601 2Pout·2Bout A1884, A1885, A1886, A1887, A1888, A1889 A:A1394, A:A918 A:A918, A:A919 2z4n B2963 2Pout·2Bout B3292, B3293, B3294, B3295, B3296, B3297 G:B1653, G:B2819 G:B2822, A:B2821 3df1 A2150 2Pout·2Bout A4151, A4152, A4153, A4154, A4155, A4156 A:A373, A:A374 C:A386, G:A377 3df2 B3543 2Pout·2Bout B4544, B4545, B4546, B4547, B4548, B4549 A:B1000, A:B1001 G:B1003, G:B1002 3df3 A2346 2Pout·2Bout A4347, A4348, A4349, A4350, A4351, A4352 A:A1394, A:A918 A:A918, A:A919 3df4 B3351 2Pout·2Bout B4352, B4353, B4354, B4355, B4356 A:B2311, C:B2310 G:B2303, G:B2304 3dil A229 2Pout·2Bout A1240, A1241, A1242, A1243, A1244 A:A23, A:A66 U:A24, G:A25 3i1n A2996 2Pout·2Bout A3473, A3474, A3475, A3476, A3477, A3478 G:A1422, G:A1423 G:A1423, G:A1425 3i1o A1541 2Pout·2Bout A1622, A1623, A1624, A1625, A1626, A1627 G:A803, U:A804 G:A771, G:A773 3i1o A4 2Pout·2Bout A1588, A1589, A1590, A1591, A1592, A1593 A:A415, G:A416 G:A417, G:A416 3i1p A3003 2Pout·2Bout A3504, A3505, A3506, A3507, A3508 A:A2705, C:A2704 A:A2705, A:A2706 3i1q A1544 2Pout·2Bout A1624, A1625, A1626, A1627, A1628, A1629 G:A803, U:A804 G:A771, U:A772 3i1q A1537 2Pout·2Bout A1590, A1591, A1592, A1593, A1594, A1595 A:A415, G:A416 G:A417, G:A425 3i1r A3022 2Pout·2Bout A3581, A3582, A3583, A3584, A3585, A3586 A:A1000, A:A1001 G:A1002, G:A1003 3i1r A3036 2Pout·2Bout A3639, A3640, A3641, A3642, 4779, 4784 A:A2740, A:A2741 G:A2742, U:A2743 3i1r A2916 2Pout·2Bout A3100, A3101, A3102, A3103, A3104, A3105 G:A831, C:A944 A:A945, A:A2448 3i1r A3038 2Pout·2Bout A3644, A3645, A3646, A3647, A3648, A3649 G:A2004, A:A1650 G:A1651, G:A1649 3i1r A3018 2Pout·2Bout A3563, A3564, A3565, A3566, A3567, A3568 C:A687, U:A686 G:A771, G:A770 3i1r A2996 2Pout·2Bout A3472, A3473, A3474, A3475, A3476, A3477 G:A1422, G:A1423 G:A1423, G:A1425 3i1s A1 2Pout·2Bout A1573, A1574, A1575, A1576, T87, T88 G:A258, G:A259 G:A260, G:A259 3i1s A1541 2Pout·2Bout A1622, A1623, A1624, A1625, A1626, A1627 G:A803, U:A804 G:A771, G:A773 3i1t A2963 2Pout·2Bout A3317, A3318, A3319, A3320, A3321, A3322 G:A1959, A:A1936 G:A1959, A:A1960 3i1t A3033 2Pout·2Bout A3617, A3618, A3619, A3620, A3621, A3622 G:A1903, G:A2597 G:A2595, U:A1971 3i1t A2968 2Pout·2Bout A3343, A3344, A3345, A3346, A3347, A3348 A:A2051, G:A2578 A:A2051, A:A2614 3i1t A3034 2Pout·2Bout A3623, A3624, A3625, A3626, 4758, 4763 G:A2742, A:A2741 G:A2742, U:A2743

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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