MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs8:B2932, See in JSmolClick on the image to toggle views Site type: 3Pout Schematic drawing for 3Pout List of all 207 Mg2+ binding sites with the site type 3Pout 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 9 | « 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 2qov B3004 3Pout B3469, B3470, B3471, B3472, B3473, B3474 G:B205, C:B383, C:B385 2qov B2921 3Pout B3091, B3092, B3093, B3094, B3095, B3096 G:B822, C:B965, A:B947 2qow A1587 3Pout A2100, A2101, A2102, A2103, N266, N1813 G:A1048, U:A1049, A:A1204 2qow A1548 3Pout A1907, A1908, A1909, A1910, A1911, A1912 U:A14, A:A16, G:A15 2qox B2967 3Pout B3320, B3321, B3322, B3323, B3324, B3325 C:B560, G:B2038, A:B1008 2qoy A1594 3Pout A2146, A2147, A2148, A2149, A2150 C:A536, C:A503, G:A537 2qoz B2921 3Pout B3585, B3586, B3587, B3588, B3589, B3590 A:B947, G:B822, C:B965 2qp0 A1587 3Pout A2098, A2099, A2100, A2101, A2102, N268 A:A1204, G:A1048, U:A1049 2qp0 A1548 3Pout A1908, A1909, A1910, A1911, A1912, A1913 U:A14, U:A13, G:A15 2qp1 B2968 3Pout B3829, B3830, B3831, B3832, B3833, B3834 C:B560, A:B1008, G:B559 2qp1 B2932 3Pout B3656, B3657, B3658, B3659, B3660, B3661 C:B965, G:B822, A:B947 2z4k A1595 3Pout A1851, A1852, A1853, A1854, A1855 C:A504, C:A536, G:A537 2z4l B3005 3Pout B3467, B3468, B3469, B3470, B3471, B3472 G:B205, C:B383, C:B385 2z4l B2922 3Pout B3090, B3091, B3092, B3093, B3094, B3095 A:B947, G:B822, C:B965 2z4m A1549 3Pout A1628, A1629, A1630, A1631, A1632, A1633 A:A16, U:A14, G:A15 3df1 A2277 3Pout A4278, A4279, A4280, A4281, A4282, A4283 C:A25, A:A553, U:A552 3df1 N2070 3Pout A4071, A4075, A4076, N4072, N4073, N4074 A:A1204, G:A1048, C:A1203 3df2 B3295 3Pout B4296, B4297, B4298, B4299, B4300, B4301 G:B578, U:B2016, U:B2017 3df3 A2029 3Pout A4030, A4031, A4032, A4033, A4034, A4035 A:A16, U:A14, G:A15 3i1p A2929 3Pout A3164, A3165, A3166, C273 G:A2599, G:A784, G:A2588 3i1p A3038 3Pout A3635, A3636, A3637, A3638, N777, N780 C:A2874, G:A2838, G:A2819 3i1q A1550 3Pout A1653, A1654, A1655, A1656, N128, N132 C:A1203, A:A1204, G:A1048 3i1s A1547 3Pout A1653, A1654, A1655, A1656, A1657, N130 A:A1204, G:A1048, U:A1049 3i20 A2965 3Pout A3326, A3327, A3328, A3329, A3330, A3331 A:A2051, G:A2578, C:A2050 3i20 A2914 3Pout A3089, A3090, A3091, A3092, A3093, A3094 G:A559, C:A560, A:A1008

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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