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 10 of 14 | « Previous | Next » | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4gau A3088 3Bout A3620, A3621, A3622, A3623, A3624, A3625 U:A1411, A:A1590, G:A1410 4tpd A3092 3Bout A3624, A3625, A3626, A3627, A3628, A3629 U:A1411, U:A1412, G:A1410 4tp5 A3092 3Bout A3623, A3624, A3625, A3626, A3627, A3628 U:A1411, G:A1410, A:A1591 4tpf A3093 3Bout A3617, A3618, A3619, A3620, A3621, A3622 G:A1410, U:A1411, U:A1409 4tp7 A3093 3Bout A3614, A3615, A3616, A3617, A3618, A3619 G:A1410, U:A1411, U:A1409 4tp9 A3093 3Bout A3621, A3622, A3623, A3624, A3625, A3626 U:A1411, U:A1412, G:A1410 4tom A3094 3Bout A3636, A3637, A3638, A3639, A3640, A3641 G:A1465, U:A1466, G:A1464 4tp9 A3096 3Bout A3637, A3638, A3639, A3640, A3641, A3642 G:A1465, U:A1466, G:A1464 4tp1 A3096 3Bout A3638, A3639, A3640, A3641, A3642, A3643 G:A1465, U:A1466, G:A1464 4tox A3096 3Bout A3634, A3635, A3636, A3637, A3638, A3639 G:A1465, U:A1466, G:A1464 4tp1 A3100 3Bout A3658, A3659, A3660, A3661, A3662, A3663 G:A1823, G:A1824, U:A1796 4too A3103 3Bout A3666, A3667, A3668, A3669, A3670, A3671 C:A2047, G:A2049, G:A2618 4tox A3104 3Bout A3671, A3672, A3673, A3674, A3675, A3676 G:A2049, G:A2048, G:A2618 2qam B3117 3Bout B3706, B3707, B3708, B3709, B3710, B3711 A:B756, A:B739, G:B757 2qba B3117 3Bout B3706, B3707, B3708, B3709, B3710, B3711 A:B756, A:B739, G:B757 4qcu A3127 3Bout A4042, A4043, A4044, A4045, P101 G:A44, G:A396, C:A43 4tpf A3132 3Bout A3781, A3782, A3783, A3784, C307, C308 U:A1825, C:A1793, G:A1826 4tp7 A3132 3Bout A3778, A3779, A3780, A3781, C310, C311 U:A1825, C:A1793, G:A1826 4too A3132 3Bout A3777, A3778, A3779, A3780, A3781, A3782 U:A1825, G:A1826, U:A1827 4tox A3132 3Bout A3782, A3783, A3784, A3785, A3786, C307 C:A1793, U:A1825, G:A1826 4qd0 A3137 3Bout A4093, A4094, A4095, A4096, A4097 A:A684, G:A682, G:A683 4qcy A3147 3Bout A4041, A4042, A4043, A4044, A4045 G:A44, G:A396, C:A43 4nvu A3155 3Bout A4032, A4033, A4034, A4035 G:A44, U:A45, G:A396 4nvy A3155 3Bout A4033, A4034, A4035, P101 G:A44, U:A45, G:A396 3df2 B3240 3Bout B4241, B4242, B4243, B4244, B4245 G:B2303, U:B2302, G:B2304

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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