MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qal:A2136, See in JSmolClick on the image to toggle views Site type: 3Pout·Rout Schematic drawing for 3Pout·Rout List of all 51 Mg2+ binding sites with the site type 3Pout·Rout 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 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1vs6 B2955 3Pout·Rout B3256, B3257, B3258, B3259, E203, E204 U:B2017, U:B2016, G:B579 U:B1255 1vs6 B2908 3Pout·Rout B3031, B3032, B3033, B3034, B3035, B3036 C:B560, A:B1008, G:B559 C:B1007 1vt2 A3023 3Pout·Rout A3579, A3580, A3581, A3582 U:A790, C:A791, C:A787 U:A790 2aw4 B2921 3Pout·Rout B3089, B3090, B3091, B3092, B3093, B3094 A:B947, C:B965, G:B822 C:B946 2awb B2967 3Pout·Rout B3318, B3319, B3320, B3321, J424, J426 G:B559, A:B1008, C:B560 C:B1007 2i2t B2955 3Pout·Rout B3262, B3263, B3264, B3265, B3266, B3267 G:B579, U:B2016, U:B2017 U:B1255 2i2v B2936 3Pout·Rout B3179, B3180, B3181, B3182, B3183, B3184 U:B2016, U:B2017, A:B2058 U:B1255 2qal A2136 3Pout·Rout A2137, A2138, A2139, A2140, A2141, A2142 U:A854, G:A727, C:A726 C:A853 2qbc B3375 3Pout·Rout B3925, B3926, B3927, B3928, B3929, B3930 C:B560, A:B1008, G:B559 C:B1007 2qbh A1589 3Pout·Rout A1823, A1824, A1825, A1826, A1827, A1828 C:A25, U:A552, A:A553 G:A524 2qbk B2968 3Pout·Rout B3321, B3322, B3323, B3324, B3325, B3326 C:B560, A:B1008, G:B559 C:B1007 2qbk B2936 3Pout·Rout B3169, B3170, B3171, B3172, B3173, B3174 G:B579, U:B2016, G:B578 U:B1255 2qov B2968 3Pout·Rout B3315, B3316, B3317, B3318, B3319, B3320 C:B1351, G:B1377, C:B1376 U:B1352 2qoz B3004 3Pout·Rout B3959, B3960, B3961, B3962, B3963, B3964 G:B205, C:B385, U:B202 C:B253 2z4k A1566 3Pout·Rout A1712, A1713, A1714, A1715, A1716, A1717 U:A854, G:A727, C:A726 C:A853 2z4l B2956 3Pout·Rout B3252, B3253, B3254, B3255, B3256, B3257 G:B578, U:B2016, U:B2017 U:B1255 3i1m A1574 3Pout·Rout A1764, A1765, A1766, A1767, A1768, L240 C:A504, C:A536, C:A503 C:A522 3i1o A1570 3Pout·Rout A1761, A1762, A1763, A1764, A1765 A:A523, C:A536, C:A503 C:A522 3i1p A2984 3Pout·Rout A3418, A3419, A3420, A3421, C533 G:A2588, A:A2587, A:A2600 A:A2439 3i1q A1574 3Pout·Rout A1759, A1760, A1761, A1762, A1763, L240 C:A504, C:A536, C:A503 C:A522 3i1r A2918 3Pout·Rout A3111, A3112, A3113, A3114, A3115, A3116 G:A579, U:A2016, G:A578 U:A1255 3i1r A2914 3Pout·Rout A3089, A3090, A3091, A3092, A3093, A3094 G:A559, C:A560, A:A1008 C:A1007 3i1z A1574 3Pout·Rout A1762, A1763, A1764, A1765, A1766, L240 C:A504, C:A536, C:A503 C:A522 3i20 A2918 3Pout·Rout A3111, A3112, A3113, A3114, A3115, A3116 G:A579, U:A2016, G:A578 U:A1255 3oaq A1574 3Pout·Rout A1764, A1765, A1766, A1767, A1768, A1769 C:A504, C:A503, C:A536 C:A522

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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