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 4 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 3i1z A1535 2Pout·2Bout A1583, A1584, A1585, A1586, A1587, A1588 A:A329, A:A315 G:A318, G:A319 3i1z A1544 2Pout·2Bout A1627, A1628, A1629, A1630, A1631, A1632 G:A803, U:A804 G:A771, U:A772 3i20 A2996 2Pout·2Bout A3472, A3473, A3474, A3475, A3476, A3477 G:A1422, G:A1423 G:A1423, G:A1425 3i20 A3022 2Pout·2Bout A3582, A3583, A3584, A3585, A3586, A3587 A:A1000, A:A1001 G:A1002, G:A1003 3i20 A3018 2Pout·2Bout A3564, A3565, A3566, A3567, A3568, A3569 C:A687, U:A686 G:A771, G:A770 3i20 A3038 2Pout·2Bout A3644, A3645, A3646, A3647, A3648, A3649 A:A1650, G:A2004 G:A1651, A:A1650 3i21 A1552 2Pout·2Bout A1675, A1676, A1677, A1678, A1679, A1680 G:A266, G:A265 G:A257, G:A259 3i21 A1541 2Pout·2Bout A1622, A1623, A1624, A1625, A1626, A1627 G:A803, U:A804 G:A771, G:A773 3i21 A1 2Pout·2Bout A1573, A1574, A1575, A1576, T87, T88 G:A258, G:A259 G:A260, G:A259 3i22 A3002 2Pout·2Bout A3507, A3508, A3509, A3510, A3511 A:A2705, C:A2704 A:A2705, A:A2706 3oaq A1 2Pout·2Bout A1577, A1578, A1579, A1580, A1581, A1582 G:A259, G:A258 G:A259, G:A260 3oaq A1537 2Pout·2Bout A1593, A1594, A1595, A1596, A1597, A1598 A:A415, G:A416 G:A417, G:A416 3oar A1549 2Pout·2Bout A1647, A1648, A1649, A1650, N101, N102 A:A1360, C:A1359 C:A980, A:A1360 3oas A2921 2Pout·2Bout A3127, A3128, A3129, A3130, A3131, A3132 A:A616, A:A608 G:A618, G:A619 3oat A2993 2Pout·2Bout A3453, A3454, A3455, A3456, A3457, A3458 G:A1421, G:A1422 G:A1423, G:A1425 3oat A3020 2Pout·2Bout A3564, A3565, A3566, A3567, A3568, A3569 A:A1000, A:A1001 G:A1002, G:A1003 3ofa A1 2Pout·2Bout A1576, A1577, A1578, A1579, A1580, A1581 G:A259, G:A258 G:A260, G:A259 3ofc A2994 2Pout·2Bout A3466, A3467, A3468, A3469, A3470, A3471 G:A1421, G:A1422 G:A1423, G:A1425 3ofc A2986 2Pout·2Bout A3428, A3429, A3430, A3431, A3432, A3433 G:A976, G:A977 G:A977, G:A978 3ofd A2921 2Pout·2Bout A3127, A3128, A3129, A3130, A3131, A3132 A:A616, A:A608 G:A618, G:A619 3ofo A1544 2Pout·2Bout A1625, A1626, A1627, A1628, A1629, A1630 G:A803, U:A804 G:A771, U:A772 3ofp A1535 2Pout·2Bout A1578, A1579, A1580, A1581, A1582, A1583 A:A315, A:A329 G:A319, G:A318 3ofq A2922 2Pout·2Bout A3126, A3127, A3128, A3129, A3130, A3131 A:A616, A:A608 G:A618, G:A619 3ofq A2992 2Pout·2Bout A3454, A3455, A3456, A3457, A3458, A3459 G:A976, G:A977 G:A977, G:A978 3ofq A2953 2Pout·2Bout A3266, A3267, A3268, A3269, A3270 G:A1456, A:A1453 G:A1456, U:A1457

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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