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 1 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 1vs5 A1598 3Pout·Bout A1866, A1867, A1868, A1869, A1870, A1871 A:A919, A:A1394, A:A918 A:A919 1vs7 A1574 3Pout·Bout A1757, A1758, A1759, A1760, A1761, A1762 A:A768, C:A805, A:A767 G:A769 1vs8 B2920 3Pout·Bout B3090, B3091, B3092, B3093, B3094, B3095 C:B1376, U:B1352, C:B1351 G:B1377 1vt2 A2949 3Pout·Bout A3249, A3250, A3251, A3252, A3253, A3254 C:A1351, C:A1376, G:A1377 G:A1377 2avy A1597 3Pout·Bout A1862, A1863, A1864, A1865, A1866, A1867 A:A919, A:A1394, A:A918 A:A919 2aw4 B2968 3Pout·Bout B3311, B3312, B3313, B3314, B3315, B3316 C:B1376, U:B1352, C:B1351 G:B1377 2aw4 B2931 3Pout·Bout B3140, B3141, B3142, B3143, B3144, B3145 A:B1937, A:B1936, G:B1959 G:B1959 2aw7 A1573 3Pout·Bout A1759, A1760, A1761, A1762, A1763, A1764 A:A768, C:A805, A:A767 G:A769 2awb B2910 3Pout·Bout B3042, B3043, B3044, B3045, B3046, B3047 C:B1986, A:B1987, C:B2551 G:B1954 2awb B2920 3Pout·Bout B3091, B3092, B3093, B3094, B3095, B3096 C:B1376, U:B1352, C:B1351 G:B1377 2i2p A1569 3Pout·Bout A1736, A1737, A1738, A1739, A1740 A:A768, A:A767, U:A804 G:A769 2i2t B2935 3Pout·Bout B3169, B3170, B3171, B3172, B3173, B3174 C:B2050, A:B2051, A:B2614 A:B2614 2qam B3369 3Pout·Bout B3912, B3913, B3914, B3915, B3916, B3917 C:B1376, G:B1377, C:B1351 G:B1377 2qan E2155 3Pout·Bout A2156, A2158, A2159, A2160, E2157 U:A20, G:A21, U:A561 G:A21 2qao B3092 3Pout·Bout B3693, B3694, B3695, B3696, B3697, B3698 C:B1351, G:B1377, C:B1376 G:B1377 2qb9 A2164 3Pout·Bout A2490, A2491, A2492, A2493, A2494 A:A767, A:A768, U:A804 G:A769 2qba B3369 3Pout·Bout B3909, B3910, B3911, B3912, B3913, B3914 C:B1376, C:B1351, G:B1377 G:B1377 2qbc B3092 3Pout·Bout B3695, B3696, B3697, B3698, B3699, B3700 C:B1376, C:B1351, G:B1377 G:B1377 2qbd A2129 3Pout·Bout A2131, A2133, A2134, A2135, E2130, E2132 G:A21, U:A20, U:A561 G:A21 2qbe B3282 3Pout·Bout B3841, B3842, B3843, B3844, B3845, L284 C:B944, G:B831, U:B568 A:B945 2qbe B3157 3Pout·Bout B3740, B3741, B3742, B3743, B3744, B3745 A:B1937, A:B1936, G:B1959 G:B1959 2qbe B3369 3Pout·Bout B3909, B3910, B3911, B3912, B3913, B3914 C:B1376, G:B1377, C:B1351 G:B1377 2qbg B2920 3Pout·Bout B3092, B3093, B3094, B3095, B3096, B3097 C:B1376, C:B1351, G:B1377 G:B1377 2qbg B2987 3Pout·Bout B3413, B3414, B3415, B3416, B3417, B3418 U:B2613, A:B2614, G:B2578 A:B2051 2qbh A1569 3Pout·Bout A1731, A1732, A1733, A1734, A1735 A:A768, U:A804, A:A767 G:A769

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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