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 3 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 3i20 A2916 3Pout·2Bout A3100, A3101, A3102, A3103, A3104, A3105 U:A568, G:A831, C:A944 A:A945, A:A2448 3i21 A2 3Pout·2Bout A1577, A1578, A1579, A1580, A1581, A1582 A:A315, A:A329, G:A319 A:A320, G:A319 3i22 A2962 3Pout·2Bout A3316, A3317, A3318, A3319, A3320, A3321 A:A1937, G:A1959, A:A1936 G:A1959, A:A1960 3ofq A2968 3Pout·2Bout A3342, A3343, A3344, A3345, A3346, A3347 A:A2051, G:A2578, C:A2050 A:A2051, A:A2614 3ofq A2986 3Pout·2Bout A3428, A3429, A3430, A3431 A:A217, A:A218, A:A428 A:A218, A:A219 3ofr A2917 3Pout·2Bout A3101, A3102, A3103, A3104, A3105, L145 C:A944, G:A831, U:A568 A:A945, A:A2448 3og0 A2966 3Pout·2Bout A3339, A3340, A3341, A3342, A3343, A3344 C:A2050, A:A2051, G:A2578 A:A2051, A:A2614 3orb A2994 3Pout·2Bout A3465, A3466, A3467, A3468, A3469, A3470 A:A1572, G:A1422, G:A1423 G:A1423, G:A1425 3owz A115 3Pout·2Bout A141, A142, A143, A144, A145, A146 U:A23, C:A24, G:A25 G:A25, G:A26 3r8s A2916 3Pout·2Bout A3158, A3159, A3160, A3161, A3162, L145 U:A568, G:A831, C:A944 A:A945, A:A2448 3r8t A2916 3Pout·2Bout A3128, A3129, A3130, A3131, A3132, L146 C:A944, G:A831, U:A568 A:A2448, A:A945 3v23 A3397 3Pout·2Bout A4259, A4260, A4261, A4262, A4263 G:A1332, G:A1334, U:A1313 G:A1334, U:A1335 3v23 B211 3Pout·2Bout B313, B314, B315, B316, B317 U:B74, A:B100, G:B75 G:B75, G:B76 3v23 A3599 3Pout·2Bout A4988, A4989, A4990, A4991, A4992, A4993 A:A1373, A:A1354, A:A1353 G:A1355, G:A1356 3v23 A3309 3Pout·2Bout A3920, A3921, A3922, A3923, A3924, P303 G:A831, G:A944, U:A568 A:A945, A:A2448 3v23 A3586 3Pout·2Bout A4916, A4917, A4918, A4919, A4920, A4921 A:A1632, G:A1633, G:A1630 C:A1631, G:A1630 3v23 A3345 3Pout·2Bout A4052, A4053, A4054, A4055, A4056, A4057 C:A1318, A:A1331, C:A1330 C:A1318, G:A1319 3v23 A3452 3Pout·2Bout A4458, A4459, A4460, A4461, A4462 U:A1357, C:A1370, G:A1358 G:A1358, G:A1371 3v25 A3264 3Pout·2Bout A3607, A3608, A3609, A3610, A3611 G:A1334, U:A1313, G:A1332 U:A1335, G:A1334 3v25 A3279 3Pout·2Bout A3670, A3671, A3672, A3673, A3674, P301 G:A831, G:A944, U:A568 A:A2448, A:A945 3v26 A1722 3Pout·2Bout A2000, A2001, A2002, A2003 A:A780, G:A799, G:A800 G:A800, A:A780 3v27 A3594 3Pout·2Bout A5046, A5047, A5048, A5049 G:A2532, A:A2533, A:A2534 A:A2534, G:A2535 3v27 A3324 3Pout·2Bout A3919, A3920, A3921, A3922, A3923, P301 G:A831, G:A944, U:A568 A:A945, A:A2448 3v27 A3451 3Pout·2Bout A4435, A4436, A4437, A4438, A4439, A4440 G:A1332, C:A1333, U:A1313 U:A1335, G:A1334 3v29 A3337 3Pout·2Bout A3768, A3769, A3770, A3771, A3772 U:A1313, G:A1334, G:A1332 U:A1335, G:A1334

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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