MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbd:A2328, See in JSmolClick on the image to toggle views Site type: 3Pout·2Bout Schematic drawing for 3Pout·2Bout List of all 131 Mg2+ binding sites with the site type 3Pout·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 5 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4ji6 A1912 3Pout·2Bout A3087, A3088, A3089, A3090, A3091, A3092 C:A868, G:A869, G:A858 G:A858, G:A869 4ji7 A2014 3Pout·2Bout A3571, A3572, A3573, A3574, A3575, A3576 G:A758, G:A581, U:A580 G:A581, G:A758 4ji8 A1979 3Pout·2Bout A3360, A3361, A3362, A3363, A3364, A3365 G:A758, U:A580, G:A581 G:A581, G:A758 4kiz A3013 3Pout·2Bout A3260, A3261, A3262, A3263, A3264, A3776 G:A831, U:A568, C:A944 A:A945, A:A2448 4nvx A3429 3Pout·2Bout A4468, A4469, A4470, P306 G:A831, G:A944, U:A568 A:A945, A:A2448 4nvz A3400 3Pout·2Bout A4317, A4318, A4319, A4320, A4321 G:A1378, U:A1359, C:A1379 U:A1381, G:A1380 4nw0 A3152 3Pout·2Bout A4153, A4154, A4155, A4156 U:A580, G:A581, G:A758 G:A581, G:A758 4pec A3013 3Pout·2Bout A3258, A3259, A3260, A3261, A3262, L301 C:A944, G:A831, U:A568 A:A2448, A:A945 4qcn A3379 3Pout·2Bout A4304, A4305, A4306, A4307, A4308 G:A1378, C:A1379, U:A1359 U:A1381, G:A1380 4qcn A3568 3Pout·2Bout A4903, A4904, A4905, A4906, A4907, P3106 G:A878, G:A989, U:A591 A:A990, A:A2460 4qcn B3013 3Pout·2Bout B3120, B3121, B3122, B3123, B3124 A:B100, U:B74, G:B75 G:B76, U:B77 4qcn A3678 3Pout·2Bout A5138, A5139, A5140, A5141, A5142, A5143 C:A1006, G:A1007, A:A1005 G:A1007, U:A1008 4qco A3141 3Pout·2Bout A3310, A3311, A3312, A3313 U:A580, G:A581, G:A758 G:A581, G:A758 4qcq A3117 3Pout·2Bout A4019, A4020, A4021, A4022, A4023 C:A779, A:A780, G:A799 G:A800, A:A780 4qcr A3590 3Pout·2Bout A4922, A4923, A4924, A4925, A4926, P308 G:A878, G:A989, U:A591 A:A990, A:A2460 4qcr A3433 3Pout·2Bout A4439, A4440, A4441, A4442, A4443 G:A1404, U:A1403, C:A1416 G:A1404, G:A1417 4qct A3467 3Pout·2Bout A4581, A4582, A4583, P308 G:A831, G:A944, U:A568 A:A945, A:A2448 4qcu A3117 3Pout·2Bout A4021, A4022, A4023, A4024 C:A779, A:A780, G:A799 G:A800, A:A780 4qcv A3543 3Pout·2Bout A4706, A4707, A4708, A4709, A4710, P306 G:A878, G:A989, U:A591 A:A990, A:A2460 4qcx A3323 3Pout·2Bout A4149, A4150, A4151, A4152 G:A1334, U:A1313, C:A1333 U:A1335, G:A1334 4qcz A3573 3Pout·2Bout A4834, A4835, A4836, A4837, A4838, P3106 G:A878, G:A989, U:A591 A:A990, A:A2460 4qcz A3564 3Pout·2Bout A4807, A4808, A4809, A4810, A4811 A:A1679, G:A1680, U:A1675 G:A1676, C:A1677 4tom A3056 3Pout·2Bout A3457, A3458, A3459, A3460, A3461, A3462 A:A1937, A:A1936, G:A1959 G:A1959, A:A1960 4too A3128 3Pout·2Bout A3759, A3760, A3761, A3762, A3763 C:A1675, A:A1676, A:A1677 A:A1676, A:A1677 4tp3 A3129 3Pout·2Bout A3770, A3771, A3772, A3773, A3774, A3775 G:A570, A:A973, U:A569 A:A820, A:A821

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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