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 2 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 2qbk B2920 3Pout·Bout B3091, B3092, B3093, B3094, B3095, B3096 C:B1376, C:B1351, G:B1377 G:B1377 2qbk B2910 3Pout·Bout B3043, B3044, B3045, B3046, B3047, B3048 A:B1669, A:B1987, C:B2551 G:B1954 2qou A1569 3Pout·Bout A2029, A2030, A2031, A2032, A2033 A:A767, A:A768, U:A804 G:A769 2qou A1559 3Pout·Bout A1974, A1975, A1976, A1977, A1978, A1979 A:A16, U:A13, U:A14 U:A14 2qov B2970 3Pout·Bout B3326, B3327, B3328, B3329, B3330, B3331 C:B1986, C:B2551, A:B1669 G:B1954 2qow E291 3Pout·Bout A2117, A2118, A2119, E295, E297, E1832 U:A561, U:A20, G:A21 G:A21 2qox B2910 3Pout·Bout B3041, B3042, B3043, B3044, B3045, B3046 C:B1986, C:B2551, A:B1669 G:B1954 2qox B2920 3Pout·Bout B3089, B3090, B3091, B3092, B3093, B3094 C:B1351, G:B1377, C:B1376 G:B1377 2qoy A1598 3Pout·Bout A2164, A2165, A2166, A2167, A2168, A2169 A:A1394, G:A917, A:A918 A:A919 2qoz B2935 3Pout·Bout B3654, B3655, B3656, B3657, B3658, B3659 C:B2050, A:B2051, G:B2578 A:B2614 2z4k A1599 3Pout·Bout A1869, A1870, A1871, A1872, A1873, A1874 A:A1394, G:A917, A:A918 A:A919 2z4k A1551 3Pout·Bout A1640, A1641, A1642, A1643, A1644, A1645 A:A315, U:A317, C:A316 G:A318 2z4l B2969 3Pout·Bout B3313, B3314, B3315, B3316, B3317, B3318 G:B1377, C:B1376, C:B1351 G:B1377 2z4m E167 3Pout·Bout A1727, A1728, A1729, A1730, E171 U:A20, G:A21, U:A561 G:A21 2z4n B2921 3Pout·Bout B3091, B3092, B3093, B3094, B3095, B3096 C:B1351, G:B1377, C:B1376 G:B1377 2z4n B2964 3Pout·Bout B3298, B3299, B3300, B3301, B3302, B3303 U:B1915, A:B1916, A:B1913 A:B1916 3df2 B3369 3Pout·Bout B4370, B4371, B4372, B4373, B4374, B4375 C:B1376, C:B1351, G:B1377 G:B1377 3df2 B3021 3Pout·Bout B4022, B4023, B4024, B4025, B4026, B4027 C:B560, A:B1008, G:B2038 A:B1008 3df4 B3092 3Pout·Bout B4093, B4094, B4095, B4096, B4097, B4098 C:B1376, C:B1351, G:B1377 G:B1377 3i1p A2953 3Pout·Bout A3264, A3265, A3266, A3267, A3268 G:A1456, A:A1453, G:A1455 G:A1456 3i1r A2965 3Pout·Bout A3326, A3327, A3328, A3329, A3330, A3331 A:A2051, G:A2578, C:A2050 A:A2051 3i1z A1552 3Pout·Bout A1663, A1664, A1665, A1666, A1667, E167 G:A1077, G:A1079, U:A1076 G:A1077 3i20 A2951 3Pout·Bout A3258, A3259, A3260, A3261, A3262 G:A1455, G:A1456, A:A1453 U:A1457 3i22 A2948 3Pout·Bout A3249, A3250, A3251, A3252, A3253, A3254 C:A1351, C:A1376, G:A1377 G:A1377 3i22 A2967 3Pout·Bout A3342, A3343, A3344, A3345, A3346, A3347 A:A2051, G:A2578, C:A2050 A:A2614

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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