MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2u:A1552, See in JSmolClick on the image to toggle views Site type: 5Bout Schematic drawing for 5Bout List of all 45 Mg2+ binding sites with the site type 5Bout 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 2 of 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4dr5 A1829 5Bout A2363, A2364, A2365, A2366, A2367, A2368 G:A21, G:A11, U:A12, G:A22, C:A23 4duz A1770 5Bout A2076, A2077, A2078, A2079, A2080, A2081 G:A664, G:A742, G:A741, G:A666, U:A740 4gar A3129 5Bout A3785, A3786, A3787, A3788, A3789, A3790 G:A1792, C:A1793, U:A1827, U:A1825, G:A1826 4gau A3001 5Bout A3201, A3202, A3203, A3204, A3205, A3206 G:A17, U:A18, A:A19, U:A521, A:A522 4ji7 A1978 5Bout A3371, A3372, A3373, A3374, A3375, A3376 C:A43, G:A44, U:A45, G:A396, C:A395 4nvv A3526 5Bout A4641, A4642, A4643, A4644, A4645, A4646 U:A2469, G:A2506, G:A2507, G:A2467, C:A2468 4nvx A3540 5Bout A4674, A4675, A4676, A4677 G:A2238, G:A2242, U:A2074, U:A2243, U:A2075 4nw1 A3534 5Bout A4673, A4674, A4675, A4676 G:A2238, G:A2242, U:A2074, U:A2243, U:A2075 4pe9 A1610 5Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A646, U:A593, U:A594, U:A644, G:A645 4qcr A3527 5Bout A4710, A4711, A4712, A4713, A4714, A4715 C:A2468, U:A2469, G:A2506, G:A2507, G:A2467 4qcv A3483 5Bout A4561, A4562, A4563, A4564, A4565 C:A2468, U:A2469, G:A2507, G:A2506, G:A2467 4qcx A3541 5Bout A4592, A4593, A4594, A4595, A4596, A4597 G:A2238, A:A2241, U:A2074, U:A2243, G:A2242 4too A3001 5Bout A3201, A3202, A3203, A3204, A3205, A3206 U:A521, C:A16, G:A17, U:A18, A:A522 4tov A3100 5Bout A3657, A3658, A3659, A3660, A3661, A3662 G:A1823, G:A1824, U:A1825, C:A1822, U:A1796 4tox A3022 5Bout A3299, A3300, A3301, A3302, A3303, A3304 G:A757, A:A756, A:A739, U:A755, C:A758 4tox A3017 5Bout A3274, A3275, A3276, A3277, A3278, A3279 U:A580, A:A1260, U:A1258, G:A1259, C:A581 4tp3 A3066 5Bout A3497, A3498, A3499, A3500, A3501, A3502 G:A2238, G:A2242, U:A2074, U:A2243, A:A2241 4tpb A3066 5Bout A3497, A3498, A3499, A3500, A3501, A3502 G:A2238, G:A2242, U:A2074, U:A2243, A:A2241 4tpc A1610 5Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A646, C:A647, U:A593, G:A592, G:A645 4tpf A3067 5Bout A3498, A3499, A3500, A3501, A3502, A3503 G:A2242, U:A2074, U:A2075, U:A2243, A:A2241

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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