MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2t:B2935, See in JSmolClick on the image to toggle views Site type: 3Pout·Bout Schematic drawing for 3Pout·Bout List of all 155 Mg2+ binding sites with the site type 3Pout·Bout 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 4 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4bpo A5030 3Pout·Bout A2043, A2044, A2045, A2046, A2047, A2379 U:A140, A:A141, G:A159 G:A159 4bpp A5030 3Pout·Bout A7491, A7492, A7493, A7494, A7495, A7496 U:A140, G:A159, A:A141 G:A159 4dha A3663 3Pout·Bout A4603, A4604, A4605, A4606 G:A2578, C:A2050, A:A2614 A:A2614 4dha B221 3Pout·Bout B314, B315, B316, B317 A:B102, G:B103, A:B73 G:B103 4dha A3703 3Pout·Bout A4747, A4748, A4749, A4750 A:A1986, C:A2551, A:A1669 G:A1954 4dhc A3685 3Pout·Bout A4705, A4706, A4707, A4708, A4709, A4710 A:A2657, C:A2658, G:A2659 G:A2659 4dhc A3630 3Pout·Bout A4499, A4500, A4501, A4502, A4503 G:A1987, C:A2551, A:A1669 G:A1954 4dhc A3447 3Pout·Bout A4015, A4016, A4017, A4018, A4019 U:A475, A:A478, G:A476 G:A476 4dr1 A1613 3Pout·Bout A1927, A1928, A1929, A1930, A1931 C:A620, A:A621, G:A617 G:A617 4dr2 A1625 3Pout·Bout A2024, A2025, A2026, A2027 C:A651, U:A751, G:A752 G:A752 4dr3 A1613 3Pout·Bout A1925, A1926, A1927, A1928, A1929 C:A620, A:A621, G:A617 G:A617 4dr3 A1827 3Pout·Bout A2142, A2143, A2144, A2145, A2146, A2147 C:A1103, A:A1101, C:A1100 C:A1100 4dr4 A1761 3Pout·Bout A2327, A2328, A2329, A2330 C:A458, G:A1300, C:A461 G:A459 4dr5 A1811 3Pout·Bout A2256, A2257, A2258, A2259, A2260, A2261 C:A150, G:A168, G:A167 G:A168 4dr6 A1612 3Pout·Bout A2033, A2034, A2035, A2036, A2037 C:A620, G:A617, A:A621 G:A617 4duy A1611 3Pout·Bout A1927, A1928, A1929, A1930, A1931 C:A620, A:A621, G:A617 G:A617 4duz A1611 3Pout·Bout A1923, A1924, A1925, A1926, A1927 G:A617, C:A620, A:A621 G:A617 4dv0 A1807 3Pout·Bout A2203, A2204, A2205, A2206, A2207, A2208 A:A171, G:A148, A:A149 G:A148 4dv1 A1767 3Pout·Bout A2106, A2107, A2108, A2109, A2110 C:A1103, C:A1100, A:A1101 C:A1100 4dv3 A1612 3Pout·Bout A1923, A1924, A1925, A1926, A1927 C:A620, A:A621, G:A617 G:A617 4dv4 A1612 3Pout·Bout A1926, A1927, A1928, A1929, A1930 C:A620, A:A621, G:A617 G:A617 4dv5 A1776 3Pout·Bout A2095, A2096, A2097, A2098, A2099, B401 C:A1103, C:A1100, A:A1101 C:A1100 4dv5 A1611 3Pout·Bout A1923, A1924, A1925, A1926, A1927 C:A620, A:A621, G:A617 G:A617 4dv6 A1611 3Pout·Bout A1927, A1928, A1929, A1930, D401 C:A620, A:A621, G:A617 G:A617 4dv7 A1611 3Pout·Bout A1923, A1924, A1925, A1926, A1927 G:A617, C:A620, A:A621 G:A617

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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