MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3464, See in JSmolClick on the image to toggle views Site type: 3Bout Schematic drawing for 3Bout List of all 341 Mg2+ binding sites with the site type 3Bout 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 1 of 14 | « 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 4tpf A3002 3Bout A3201, A3202, A3203, A3204, A3205, A3206 U:A521, U:A18, A:A522 4tpf A3093 3Bout A3617, A3618, A3619, A3620, A3621, A3622 G:A1410, U:A1411, U:A1409 4tpf A3132 3Bout A3781, A3782, A3783, A3784, C307, C308 U:A1825, C:A1793, G:A1826 4tpf A3017 3Bout A3274, A3275, A3276, A3277, A3278, E304 U:A1258, C:A581, G:A1259 4tpf A3027 3Bout A3315, A3316, A3317, A3318, A3319, A3320 G:A798, G:A797, C:A796 4tpe A1605 3Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A257, G:A258, G:A259 4tpd A3092 3Bout A3624, A3625, A3626, A3627, A3628, A3629 U:A1411, U:A1412, G:A1410 4tpb A3002 3Bout A3201, A3202, A3203, A3204, A3205, A3206 U:A521, G:A17, U:A18 4tp9 A3093 3Bout A3621, A3622, A3623, A3624, A3625, A3626 U:A1411, U:A1412, G:A1410 4tp9 A3096 3Bout A3637, A3638, A3639, A3640, A3641, A3642 G:A1465, U:A1466, G:A1464 4tp7 A3093 3Bout A3614, A3615, A3616, A3617, A3618, A3619 G:A1410, U:A1411, U:A1409 4tp7 A3017 3Bout A3273, A3274, A3275, A3276, A3277, E305 U:A1258, C:A581, G:A1259 4tp7 A3132 3Bout A3778, A3779, A3780, A3781, C310, C311 U:A1825, C:A1793, G:A1826 4tp5 A3026 3Bout A3319, A3320, A3321, A3322, A3323, A3324 C:A796, G:A798, G:A797 4tp5 A3092 3Bout A3623, A3624, A3625, A3626, A3627, A3628 U:A1411, G:A1410, A:A1591 4tp1 A3002 3Bout A3201, A3202, A3203, A3204, A3205, A3206 G:A17, U:A521, U:A18 4tp1 A3096 3Bout A3638, A3639, A3640, A3641, A3642, A3643 G:A1465, U:A1466, G:A1464 4tp1 A3100 3Bout A3658, A3659, A3660, A3661, A3662, A3663 G:A1823, G:A1824, U:A1796 4tp1 A3017 3Bout A3276, A3277, A3278, A3279, A3280, A3281 G:A1259, U:A580, U:A1258 4tp1 A3022 3Bout A3299, A3300, A3301, A3302, A3303, A3304 A:A756, A:A739, G:A757 4tox A3039 3Bout A3371, A3372, A3373, A3374, A3375, A3376 A:A2009, G:A2010, U:A2011 4tox A3132 3Bout A3782, A3783, A3784, A3785, A3786, C307 C:A1793, U:A1825, G:A1826 4tox A3096 3Bout A3634, A3635, A3636, A3637, A3638, A3639 G:A1465, U:A1466, G:A1464 4tox A3104 3Bout A3671, A3672, A3673, A3674, A3675, A3676 G:A2049, G:A2048, G:A2618 4tox A3002 3Bout A3201, A3202, A3203, A3204, A3205, A3206 U:A521, G:A17, U:A18

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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