MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4k:A1546, See in JSmolClick on the image to toggle views Site type: Pout·2Bout Schematic drawing for Pout·2Bout List of all 343 Mg2+ binding sites with the site type Pout·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 1 of 14 | « 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 1egk C3 Pout·2Bout B61, C28, C29, C30, C31, C32 DA:B45 A:C104, G:C105 1ehz A570 Pout·2Bout A731, A732, A733, A734, A735, A736 C:A25 U:A41, G:A42 1evv A904 Pout·2Bout A936, A937, A938, A939, A940, A941 C:A25 G:A42, U:A41 1vs5 A1557 Pout·2Bout A1666, A1667, A1668, A1669, A1670, A1671 A:A1046 G:A1047, G:A1048 1vs5 A1564 Pout·2Bout A1702, A1703, A1704, A1705, A1706, A1707 A:A781 G:A799, G:A800 1vs6 B2997 Pout·2Bout B3438, B3439, B3440, B3441, B3442, B3443 U:B686 G:B770, G:B771 1vs7 A1562 Pout·2Bout A1689, A1690, A1691, A1692, A1693, A1694 G:A1079 G:A1077, U:A1076 1vs7 A1564 Pout·2Bout A1701, A1702, A1703, A1704, A1705, A1706 A:A315 G:A319, G:A318 1vt2 A3002 Pout·2Bout A3503, A3504, A3505, A3506, A3507, A3508 C:A2616 G:A2049, C:A2047 1y26 X101 Pout·2Bout X267, X268, X269, X270, X271, X272 A:X45 G:X46, U:X47 1yls B244 Pout·2Bout B367, B368, B369, B370, B371, B372 U:B212 G:B213, U:B231 2avy A1562 Pout·2Bout A1693, A1694, A1695, A1696, A1697, A1698 G:A266 G:A257, G:A258 2avy A1556 Pout·2Bout A1665, A1666, A1667, A1668, A1669, A1670 A:A1046 G:A1047, G:A1048 2aw7 A1563 Pout·2Bout A1702, A1703, A1704, A1705, A1706, A1707 A:A315 G:A319, G:A318 2aw7 A1561 Pout·2Bout A1690, A1691, A1692, A1693, A1694, A1695 G:A1079 G:A1077, U:A1076 2i2p A1545 Pout·2Bout A1614, A1615, A1616, A1617, A1618, A1619 G:A803 G:A771, U:A772 2i2t B3018 Pout·2Bout B3531, B3532, B3533, B3534, B3535, B3536 G:B2597 G:B2595, U:B1971 2i2t B3019 Pout·2Bout B3538, B3539, B3540, 4754, 4756, 4759 A:B2740 G:B2742, U:B2743 2i2v B2957 Pout·2Bout B3276, B3277, B3278, B3279, B3280, B3281 A:B2386 C:B2326, A:B2386 2i2v B2917 Pout·2Bout B3085, B3086, B3087, B3088, B3089, B3090 A:B2033 G:B2027, U:B2028 2i2v B2969 Pout·2Bout B3337, B3338, B3339, B3340, B3341, B3342 G:B649 C:B650, G:B651 2i2v B3018 Pout·2Bout B3530, B3531, B3532, B3533, B3534, B3535 G:B2597 G:B2595, U:B1971 2otj 08100 Pout·2Bout 03788, 04283, 05543, 06186, 07847 C:02077 G:02079, G:02080 2qal A2077 Pout·2Bout A2078, A2079, A2080, A2081, A2082, A2083 A:A1046 G:A1047, G:A1048 2qan A2134 Pout·2Bout A2135, A2136, A2137, A2138, A2139, A2140 A:A1046 G:A1047, G:A1048

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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