MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2t:B2935, See in JSmolClick on the image to toggle views Site type: 3Pout·Bout Schematic drawing for 3Pout·Bout List of all 155 Mg2+ binding sites with the site type 3Pout·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 6 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 4qcp A3460 3Pout·Bout A4573, A4574, A4575, P307 G:A831, G:A944, U:A568 A:A2448 4qcp A3405 3Pout·Bout A4426, A4427, A4428, A4429, A4430, A4431 U:A2884, U:A2832, C:A2885 G:A2886 4qcr A3450 3Pout·Bout A4492, A4493, A4494, A4495 A:A2008, C:A2563, G:A2009 G:A1976 4qcr A3526 3Pout·Bout A4704, A4705, A4706, A4707, A4708, A4709 U:A2894, U:A2842, C:A2895 G:A2896 4qcr A3706 3Pout·Bout A5171, A5172, A5173, A5174, A5175 C:A1006, G:A1007, A:A1005 G:A1007 4qct A3459 3Pout·Bout A4562, A4563, A4564, 7101 G:A770, G:A686, G:A771 G:A770 4qct A3409 3Pout·Bout A4434, A4435, A4436, A4437, A4438, A4439 U:A2884, U:A2832, C:A2885 G:A2886 4qcv A3395 3Pout·Bout A4363, A4364, A4365, A4366, A4367 G:A1404, U:A1403, C:A1416 G:A1417 4qcz A3504 3Pout·Bout A4627, A4628, A4629, A4630, A4631, A4632 U:A2894, U:A2842, C:A2895 G:A2896 4qd1 A3472 3Pout·Bout A4462, A4463, A4464, P306 G:A831, G:A944, U:A568 A:A2448 4tom A3050 3Pout·Bout A3427, A3428, A3429, A3430, A3431, A3432 A:A1669, C:A1986, A:A1987 G:A1954 4ton A1636 3Pout·Bout A1864, A1865, A1866, A1867 C:A1303, G:A1304, G:A1305 G:A1305 4too A3013 3Pout·Bout A3259, A3260, A3261, A3262, A3263, L201 C:A944, U:A568, G:A831 A:A945 4too A3044 3Pout·Bout A3390, A3391, A3392, A3393, A3394, A3395 C:A1376, G:A1377, C:A1351 G:A1377 4too A3075 3Pout·Bout A3539, A3540, C305, C306, C307 A:A2587, G:A2588, A:A2589 A:A2589 4tox A3045 3Pout·Bout A3393, A3394, A3395, A3396, A3397, A3398 C:A1376, G:A1377, C:A1351 G:A1377 4tox A3014 3Pout·Bout A3258, A3259, A3260, A3261, A3262, L201 G:A831, C:A944, U:A568 A:A945 4tp3 A3063 3Pout·Bout A3484, A3485, A3486, A3487 G:A2056, G:A2057, G:A2505 A:A2058 4tp3 A3048 3Pout·Bout A3410, A3411, A3412, A3413, A3414 G:A1455, G:A1456, A:A1453 U:A1457 4tp3 A3051 3Pout·Bout A3425, A3426, A3427, A3428, A3429, A3430 A:A1669, C:A2551, A:A1987 G:A1954 4tp3 A3028 3Pout·Bout A3328, A3329, A3330, A3331, A3332 A:A802, G:A674, A:A675 A:A804 4tp3 A3014 3Pout·Bout A3260, A3261, A3262, A3263, A3264, A3265 U:A568, C:A944, G:A831 A:A945 4tp5 A3055 3Pout·Bout A3449, A3450, A3451, A3452, A3453 G:A1776, A:A1981, U:A1775 G:A1776 4tp7 A3014 3Pout·Bout A3259, A3260, A3261, A3262, A3263, L201 C:A944, G:A831, U:A568 A:A945 4tpa A1636 3Pout·Bout A1866, A1867, A1868, A1869 C:A1303, G:A1305, G:A1304 G:A1305

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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