MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs8:B2932, See in JSmolClick on the image to toggle views Site type: 3Pout Schematic drawing for 3Pout List of all 207 Mg2+ binding sites with the site type 3Pout 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 9 | « 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 3i21 A1547 3Pout A1652, A1653, A1654, A1655, A1656, N130 A:A1204, G:A1048, U:A1049 3i22 C273 3Pout A3164, A3165, A3166, C275 G:A2599, G:A784, G:A2588 3i22 A3036 3Pout A3635, A3636, A3637, A3638, A3639, N780 C:A2874, G:A2838, G:A2819 3oas A3036 3Pout A3634, A3635, A3636, A3637, A3638, N780 C:A2874, G:A2819, G:A2838 3oas A2994 3Pout A3467, A3468, A3469, A3470, A3471 A:A1027, C:A1123, A:A1028 3oas C272 3Pout A3163, A3164, A3165, A3166 G:A2599, G:A784, G:A2588 3ofc A2959 3Pout A3302, A3303, A3304, A3305 G:A1968, G:A2592, G:A1973 3ofd C272 3Pout A3163, A3164, C273, C274 G:A784, G:A2588, G:A2599 3ofd A3037 3Pout A3639, A3640, A3641, A3642, A3643, N780 C:A2874, G:A2819, G:A2838 3ofp A1550 3Pout A1652, A1653, A1654, A1655, A1656, N105 A:A1204, G:A1048, U:A1049 3ofq A3037 3Pout A3637, A3638, A3639, A3640, A3641, N780 C:A2874, G:A2819, G:A2838 3ofr A2933 3Pout A3176, A3177, A3178, A3179, A3180, A3181 G:A822, A:A947, C:A965 3og0 A3035 3Pout A3636, A3637, A3638, A3639, A3640, N780 C:A2874, G:A2838, G:A2819 3og0 C272 3Pout A3161, A3162, A3163, A3164 G:A2599, G:A784, G:A2588 3oww A107 3Pout A149, A150, A151, A152, A153, B134 G:A32, U:A67, G:B10 3owz B106 3Pout A139, A140, B117, B118, B119, B120 C:A66, A:A33, A:B33 3oxj B108 3Pout A137, B126, B127, B128, B129, B130 G:A10, G:B32, U:B67 3r8s A3040 3Pout A3711, A3712, A3713, A3714, A3715, N791 G:A2819, G:A2838, A:A2820 3td0 A1000 3Pout A1002, A1004, A1005, B1001, B1003, B1006 C:A12, C:B30, G:B31 3v22 A1698 3Pout A1910, A1911, A1912, A1913 C:A578, C:A817, G:A576 3v23 A3506 3Pout A4660, A4661, A4662, A4663 C:A2745, C:A2755, U:A2754 3v23 A3472 3Pout A4541, A4542, A4543, A4544, A4545, A4546 C:A837, C:A935, C:A838 3v23 A3355 3Pout A4095, A4096, A4097, A4098, A4099 A:A677, C:A795, G:A794 3v27 A3551 3Pout A4876, A4877, A4878, A4879, A4880 U:A2519, C:A2464, C:A2538 3v27 5103 3Pout 5201, 5202, 5203, 5204, 5205 G:A16, G:A518, G:A17

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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