MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3i20:A2945, See in JSmolClick on the image to toggle views Site type: Oph·Pout Schematic drawing for Oph·Pout List of all 1301 Mg2+ binding sites with the site type Oph·Pout 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 6 of 53 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2avy A1547 Oph·Pout C:A934(OP1) A1622, A1623, A1624, A1625, A1626 U:A1345 2aw4 B2911 Oph·Pout U:B1647(OP2) B3041, B3042, B3043, B3044, B3045 U:B1325 C:B1646, A:B1616 2aw4 B2965 Oph·Pout A:B1156(OP2) B3298, B3299, B3300, B3301, B3302 A:B1155 G:B1157, G:B997 2aw4 B2969 Oph·Pout A:B1664(OP2) B3317, B3318, B3319, B3320, B3321 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666 2aw4 B2930 Oph·Pout A:B945(OP1) B3135, B3136, B3137, B3138, B3139 G:B831 G:B831, U:B832 2aw4 B2951 Oph·Pout G:B536(OP2) B3232, B3233, B3234, B3235, B3236 G:B535 G:B537 2aw4 B2954 Oph·Pout A:B574(OP2) B3246, B3247, B3248, B3249, B3250 U:B576 U:B576, G:B577 2aw7 A1600 Oph·Pout G:A111(OP2) A1883, A1884, A1885, A1886, A1887 C:A110 G:A112 2aw7 A1594 Oph·Pout G:A100(OP2) A1855, A1856, A1857, A1858, A1859 A:A101 C:A99, G:A100, A:A101, G:A64 2aw7 A1582 Oph·Pout A:A1433(OP2) A1800, A1801, A1802, A1803, A1804 A:A1434 A:A1434, G:A1435 2aw7 A1599 Oph·Pout C:A352(OP2) A1878, A1879, A1880, A1881, A1882 G:A354 C:A330, C:A352, G:A331 C:A330, A:A59, G:A354 2aw7 A1552 Oph·Pout C:A934(OP1) A1650, A1651, A1652, A1653, A1654 U:A1345 2aw7 A1586 Oph·Pout A:A608(OP2) A1818, A1819, A1820, A1821, A1822 A:A609 A:A630, A:A609, C:A631, U:A610 2awb B2978 Oph·Pout U:B1647(OP2) B3369, B3370, B3371, B3372, B3373 A:B1272 C:B1646, A:B1616 A:B1616 2awb B3009 Oph·Pout A:B1676(OP2) B3488, B3489, B3490, B3491, B3492 C:B1675 A:B1676, A:B1677 2awb B2940 Oph·Pout A:B2270(OP2) B3190, B3191, B3192, B3193, B3194 A:B2267 G:B2271 2awb B2931 Oph·Pout A:B945(OP1) B3146, B3147, B3148, B3149, B3150 G:B831 G:B831 2awb B2926 Oph·Pout A:B1156(OP2) B3120, B3121, B3122, B3123, B3124 A:B1155 G:B1157, C:B998 2awb B2943 Oph·Pout G:B536(OP2) B3202, B3203, B3204, B3205, B3206 G:B535 G:B536, G:B537 2awb B2913 Oph·Pout A:B1664(OP2) B3058, B3059, B3060, B3061, B3062 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666, G:B1663 2awb B2950 Oph·Pout U:B120(OP1) B3234, B3235, B3236, B3237, B3238 G:B122 G:B124, G:B123 2i2p X62 Oph·Pout U:X6(OP1) A1897, X366, X367, X368, X369 U:X5 U:X2, U:X6 G:A1497, U:A1498 2i2p A1570 Oph·Pout A:A572(OP1) A1741, A1742, A1743, A1744, A1745 A:A573 A:A819 2i2p A1547 Oph·Pout C:A934(OP1) A1623, A1624, A1625, A1626, A1627 U:A1345 2i2t B2969 Oph·Pout A:B1664(OP2) B3327, B3328, B3329, B3330, B3331 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666

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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