MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbb:A2049, See in JSmolClick on the image to toggle views Site type: 2Pout·Bout Schematic drawing for 2Pout·Bout List of all 169 Mg2+ binding sites with the site type 2Pout·Bout 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 7 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 4qcr A3603 2Pout·Bout A4960, A4961, A4962, A4963, A4964 U:A2792, G:A2793 A:A553 4qcr A3503 2Pout·Bout A4635, A4636, A4637, A4638 A:A2788, C:A2787 A:A2788 4qcr A3520 2Pout·Bout A4682, A4683, A4684, A4685, A4686 A:A1399, A:A1400 G:A1402 4qcr A3614 2Pout·Bout A4991, A4992, A4993, A4994, A4995, A4996 G:A2609, G:A1926 G:A2607 4qct A3482 2Pout·Bout A4610, A4611, A4612, A4613, A4614 G:A2597, G:A1904 G:A2595 4qcv A3554 2Pout·Bout A4733, A4734, A4735, A4736, A4737, A4738 G:A2609, G:A1926 G:A2607 4qcz A3417 2Pout·Bout A4396, A4397, A4398, A4399, A4400 G:A1404, U:A1403 G:A1417 4tou A1601 2Pout·Bout A1701, A1702, A1703, A1704, A1705, T101 G:A258, G:A259 G:A260 4tov A3135 2Pout·Bout A3796, A3797, A3798, A3799, A3800, 4201 A:A2740, A:A2741 G:A2742 4tox A3134 2Pout·Bout A3790, A3791, A3792, A3793, A3794, 4201 A:A2741, A:A2740 G:A2742 4tp0 A1601 2Pout·Bout A1701, A1702, A1703, A1704, A1705, T101 G:A258, G:A259 G:A260 4tp2 A1636 2Pout·Bout A1867, A1868, A1869, A1870 C:A1303, G:A1305 G:A1305 4tp3 A3133 2Pout·Bout A3787, A3788, A3789, A3790, A3791, 4201 A:A2741, A:A2740 G:A2742 4tp7 A3134 2Pout·Bout A3786, A3787, A3788, A3789, A3790, 4201 A:A2740, A:A2741 G:A2742 4tp8 A1602 2Pout·Bout A1705, A1706, A1707, A1708, A1709, A1710 A:A329, A:A315 G:A319 4tp9 A3120 2Pout·Bout A3733, A3734, A3735, A3736, A3737, A3738 A:A1000, A:A1001 G:A1002 4tpb A3133 2Pout·Bout A3789, A3790, A3791, A3792, A3793, 4201 A:A2741, A:A2740 G:A2742 4tpc A1601 2Pout·Bout A1701, A1702, A1703, A1704, A1705, T101 G:A258, G:A259 G:A260 4tpf A3125 2Pout·Bout A3753, A3754, A3755, A3756 C:A787, U:A790 A:A1780

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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