MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs6:B2935, See in JSmolClick on the image to toggle views Site type: 4Pout·2Bout Schematic drawing for 4Pout·2Bout List of all 40 Mg2+ binding sites with the site type 4Pout·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 1 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 1vs6 B2935 4Pout·2Bout B3163, B3164, B3165, B3166, B3167, B3168 C:B2050, A:B2051, G:B2578, A:B2614 A:B2051, A:B2614 2qan A2189 4Pout·2Bout A2190, A2191, A2192, A2193, A2194, A2195 A:A768, U:A804, C:A805, A:A767 A:A768, G:A769 2qao B3026 4Pout·2Bout B3639, B3640, B3641, B3642, B3643, B3644 C:B1958, G:B1959, A:B1936, A:B1937 A:B1960, G:B1959 2qba B3181 4Pout·2Bout B3759, B3760, B3761, B3762, B3763, B3764 C:B2050, G:B2578, A:B2051, A:B2614 A:B2051, A:B2614 2qba B3157 4Pout·2Bout B3739, B3740, B3741, B3742, B3743, B3744 A:B1937, A:B1936, C:B1958, G:B1959 G:B1959, A:B1960 2qbc B3026 4Pout·2Bout B3640, B3641, B3642, B3643, B3644, B3645 A:B1937, C:B1958, A:B1936, G:B1959 A:B1960, G:B1959 2qbe B3181 4Pout·2Bout B3759, B3760, B3761, B3762, B3763, B3764 C:B2050, G:B2578, A:B2051, A:B2614 A:B2051, A:B2614 2qbf A1572 4Pout·2Bout A1757, A1758, A1759, A1760, A1761, A1762 A:A768, U:A804, C:A805, A:A767 G:A769, A:A768 2qbi B2931 4Pout·2Bout B3141, B3142, B3143, B3144, B3145, B3146 G:B1959, A:B1937, A:B1936, C:B1958 G:B1959, A:B1960 2qow A1560 4Pout·2Bout A1972, A1973, A1974, A1975, A1976, A1977 A:A768, U:A804, C:A805, A:A767 G:A769, A:A768 2qox B2909 4Pout·2Bout B3035, B3036, B3037, B3038, B3039, B3040 A:B1936, A:B1937, G:B1959, C:B1958 G:B1959, A:B1960 2qoz B2931 4Pout·2Bout B3636, B3637, B3638, B3639, B3640, B3641 G:B1959, A:B1937, A:B1936, C:B1958 G:B1959, A:B1960 2qp1 B2909 4Pout·2Bout B3542, B3543, B3544, B3545, B3546, B3547 A:B1937, G:B1959, A:B1936, C:B1958 G:B1959, A:B1960 2z4m A1573 4Pout·2Bout A1755, A1756, A1757, A1758, A1759, A1760 A:A768, U:A804, C:A805, A:A767 G:A769, A:A768 3df1 A2044 4Pout·2Bout A4045, A4046, A4047, A4048, A4049, A4050 A:A329, A:A315, U:A317, C:A316 G:A318, G:A319 3df3 A2189 4Pout·2Bout A4190, A4191, A4192, A4193, A4194, A4195 A:A768, C:A805, U:A804, A:A767 A:A768, G:A769 3r8s A2960 4Pout·2Bout A3358, A3359, A3360, A3361, A3362, A3363 C:A1958, G:A1959, A:A1936, A:A1937 G:A1959, A:A1960 3r8t A2959 4Pout·2Bout A3331, A3332, A3333, A3334, A3335, A3336 A:A1937, C:A1958, A:A1936, G:A1959 G:A1959, A:A1960 3v25 A3285 4Pout·2Bout A3693, A3694, A3695, A3696, A3697 A:A1634, G:A1627, G:A1628, U:A1300 G:A1628, U:A1629 3v28 A1752 4Pout·2Bout A2023, A2024, A2025, A2026, A2027, A2028 A:A780, G:A800, C:A779, G:A799 A:A780, G:A800 3v2d A3696 4Pout·2Bout A5676, A5677, A5678, A5679 G:A2578, A:A2051, U:A2613, A:A2614 A:A2051, A:A2614 3v2f A3601 4Pout·2Bout A5077, A5078, A5079, A5080, A5081, A5082 G:A2578, A:A2614, A:A2051, U:A2613 A:A2614, A:A2051 4dhc A3632 4Pout·2Bout A4510, A4511, A4512, A4513, A4514, A4515 G:A2578, A:A2614, A:A2051, U:A2613 A:A2614, A:A2051 4dr5 A1838 4Pout·2Bout A2414, A2415, A2416, A2417, A2418, A2419 U:A757, G:A758, U:A580, G:A581 G:A581, G:A758 4dr6 A1886 4Pout·2Bout A2778, A2779, A2780, A2781, A2782, A2783 U:A757, G:A758, U:A580, G:A581 G:A581, G:A758

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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