MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs7:A1593, See in JSmolClick on the image to toggle views Site type: 2Pout Schematic drawing for 2Pout List of all 191 Mg2+ binding sites with the site type 2Pout 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 5 of 8 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3oat A2932 2Pout A3171, A3172, A3173, A3174, A3175, A3176 G:A822, A:A947 3oas A2933 2Pout A3183, A3184, A3185, A3186, A3187, A3188 C:A965, A:A947 3oas A2961 2Pout A3309, A3310, A3311, A3312, A3313, A3314 A:A1916, U:A1915 3oas A2906 2Pout A3049, A3050, A3051, A3052, A3053, A3054 C:A41, A:A42 3oas A2914 2Pout A3087, A3088, A3089, A3090, A3091, A3092 C:A560, G:A2038 3i22 A2914 2Pout A3088, A3089, A3090, A3091, A3092, A3093 C:A560, G:A2038 3i22 A2961 2Pout A3310, A3311, A3312, A3313, A3314, A3315 A:A1916, U:A1915 3i1t A3037 2Pout A3636, A3637, A3638, A3639, A3640, N780 G:A2838, G:A2819 3i1t A2934 2Pout A3185, A3186, A3187, A3188, A3189, A3190 C:A965, G:A822 3i1t A2962 2Pout A3311, A3312, A3313, A3314, A3315, A3316 A:A1916, U:A1915 3i1p A2934 2Pout A3183, A3184, A3185, A3186, A3187, A3188 C:A965, G:A822 3i1p A2962 2Pout A3308, A3309, A3310, A3311, A3312, A3313 A:A1916, U:A1915 3i1p A2914 2Pout A3090, A3091, A3092, A3093, A3094, A3095 C:A560, G:A2038 3i1p A2947 2Pout A3239, A3240, A3241, T348, T350 U:A1313, G:A1334 3i1n A2933 2Pout A3182, A3183, A3184, A3185, A3186, A3187 G:A822, A:A947 3i1n A2951 2Pout A3260, A3261, A3262, A3263, A3264 G:A1455, A:A1453 3df4 B3165 2Pout B4166, B4167, B4168, B4169, B4170, B4171 G:B822, C:B965 3df3 A2295 2Pout A4296, A4297, A4298, A4299, A4300, A4301 U:A552, A:A553 3df2 B3096 2Pout B4097, B4098, B4099, B4100, B4101, B4102 C:B965, G:B822 3df1 A2328 2Pout A4329, A4330, A4331, A4332, A4333, A4334 A:A1394, A:A918 3cxc B8055 2Pout 04707, 07321, 08614, B8560, B8677, B8678 U:02721, C:02720 3cc2 B8055 2Pout 03311, 05993, 07283, B8551, B8663 U:02721, C:02720 2z4n B2933 2Pout B3152, B3153, B3154, B3155, B3156, B3157 G:B822, C:B965 2z4k A1590 2Pout A1827, A1828, A1829, A1830, A1831, A1832 C:A25, A:A553 2qp0 A1571 2Pout A2028, A2029, A2030, A2031, A2032, A2033 U:A552, A:A553

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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