MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3r8s:A2930, See in JSmolClick on the image to toggle views Site type: Oph Schematic drawing for Oph List of all 588 Mg2+ binding sites with the site type Oph 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 24 | « 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 1evv A903 Oph G:A19(OP1) A918, A919, A920, A921, A922 G:A20, U:A59, C:A60, C:A56 1tra A79 Oph G:A19(OP1) A175, A176, A177, A178, A179 G:A20, U:A59, C:A60 1vs5 A1572 Oph G:A21(OP1) A1743, A1744, A1745, A1746, A1747 G:A567, A:A573 1vs5 A1555 Oph A:A937(OP2) A1656, A1657, A1658, A1659, A1660 G:A939 1vs5 A1591 Oph G:A100(OP2) A1833, A1834, A1835, A1836, A1837 G:A64, C:A99, G:A100, A:A101 1vs6 B2948 Oph U:B120(OP2) B3222, B3223, B3224, B3225, B3226 G:B122, G:B123, G:B121 1vs6 B3010 Oph A:B1676(OP2) B3494, B3495, B3496, B3497, B3498 C:B1675 A:B1677, A:B1676 1vs6 B2962 Oph A:B800(OP1) B3290, B3291, B3292, B3293, B3294 A:B191, C:B192 1vs6 B2934 Oph U:B419(OP1) B3158, B3159, B3160, B3161, B3162 G:B230 1vs6 B2972 Oph A:B1678(OP2) B3336, B3337, B3338, B3339, B3340 A:B1678, A:B1679 1vs7 A1576 Oph G:A21(OP1) A1768, A1769, A1770, A1771, A1772 G:A568, G:A567 A:A573, G:A567 1vs7 A1587 Oph A:A608(OP2) A1816, A1817, A1818, A1819, A1820 A:A630, A:A609, C:A631, U:A610 1vs7 A1575 Oph A:A572(OP1) A1763, A1764, A1765, A1766, A1767 A:A819 1vs7 A1604 Oph C:A980(OP1) A1896, A1897, A1898, A1899, A1900 G:A1221, G:A1220, A:A1219 1vs7 A1565 Oph A:A937(OP2) A1707, A1708, A1709, A1710, A1711 G:A939 1vs8 B2945 Oph U:B120(OP2) B3211, B3212, B3213, B3214, B3215 G:B122, G:B123 1vs8 B2964 Oph U:B419(OP1) B3306, B3307, B3308, B3309, B3310 G:B230 1vs8 B2922 Oph A:B800(OP1) B3100, B3101, B3102, B3103, B3104 G:B799 A:B191, C:B192, A:B800 1vs8 B2946 Oph A:B1678(OP2) B3216, B3217, B3218, B3219, B3220 A:B1679 1vt2 A2922 Oph A:A621(OP2) A3133, A3134, A3135, L146 G:A620 1vt2 A2911 Oph U:A419(OP1) A3070, A3071, A3072, A3073, A3074 G:A230 1vt2 A2941 Oph A:A1156(OP2) A3214, A3215, A3216, A3217, A3218 C:A998, G:A1157, G:A997 1vt2 A2958 Oph A:A1678(OP2) A3291, A3292, A3293, A3294, A3295 A:A1678, A:A1679 1vt2 A2987 Oph A:A299(OP2) A3434, A3435, A3436, A3437, U491 A:A299, G:A338, U:A339, A:A300 1vt2 A2914 Oph G:A536(OP2) A3083, A3084, A3085, A3086, A3087

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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