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 7 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 4ji6 A1854 3Pout A2740, A2741, A2742, A2743, A2744, A2745 U:A1345, A:A1346, C:A934 4ji6 A1909 3Pout A3069, A3070, A3071, A3072, A3073, A3074 A:A964, U:A1199, G:A1198 4ji7 A1642 3Pout A2179, A2180, A2181, A2182 A:A16, U:A13, U:A14 4ji7 A1605 3Pout A2108, A2109, A2110, A2111 U:A652, C:A651, U:A751 4jnx B501 3Pout A401, A402, B611, B612, B613, B614 U:B412, G:B413, C:B411 4lfb A1820 3Pout A1909, A1910, A1911, A1912, A1913, A1914 A:A16, G:A15, U:A14 4nvx A3617 3Pout A4831, A4832, A4833, A4834 G:A2000, A:A2001, A:A1654 4nvz A3364 3Pout A4241, A4242, A4243, A4244 G:A2011, C:A2012, G:A1714 4nxm A1608 3Pout A1913, A1914, A1915, A1916 C:A651, U:A652, G:A752 4nxn A1608 3Pout A1914, A1915, A1916, A1917 C:A651, U:A652, U:A751 4pea A1631 3Pout A1843, A1844, A1845, A1846, A1847, N203 U:A1049, A:A1204, G:A1048 4peb A3034 3Pout A3360, A3361, A3362, A3363 U:A999, C:A1153, C:A998 4peb A3029 3Pout A3339, A3340, A3341, A3342, A3343, A3344 G:A822, A:A947, C:A965 4peb A3061 3Pout A3484, A3485, A3486, A3487, A3488, A3489 U:A2613, A:A2051, G:A2578 4pec A3011 3Pout A3247, A3248, A3249, A3250, A3251, A3252 A:A1008, G:A2038, C:A560 4pec A3029 3Pout A3334, A3335, A3336, A3337, A3338, A3339 G:A822, C:A965, A:A947 4pec A3136 3Pout A3804, A3805, A3806, A3807, A3808, N201 C:A2874, G:A2838, G:A2819 4pec A3085 3Pout A3589, A3590, A3591, A3592, A3593 A:A981, G:A978, C:A982 4qcs A3106 3Pout A4077, A4078, A4079, A4080 U:A13, U:A14, A:A16 4ton A1631 3Pout A1844, A1845, A1846, A1847, A1848, N203 U:A1049, A:A1204, G:A1048 4too A3137 3Pout A3799, A3800, A3801, A3802, A3803, N202 C:A2874, G:A2838, G:A2819 4too A3011 3Pout A3248, A3249, A3250, A3251, A3252, A3253 A:A1008, G:A2038, C:A560 4tov A3036 3Pout A3357, A3358, A3359, A3360 U:A999, C:A1153, C:A998 4tov A3031 3Pout A3337, A3338, A3339, A3340, A3341, A3342 G:A822, C:A965, A:A947 4tow A1631 3Pout A1843, A1844, A1845, A1846, A1847, N203 U:A1049, A:A1204, G:A1048

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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