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 7 of 53 | « Previous | Next » | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2i2t B3020 Oph·Pout A:B943(OP2) B3541, B3542, B3543, B3544, L764 U:B832 2i2t B2981 Oph·Pout A:B2270(OP2) B3383, B3384, B3385, B3386, B3387 G:B2271 G:B2271 2i2t B3010 Oph·Pout A:B1676(OP2) B3498, B3499, B3500, B3501, B3502 C:B1675 A:B1676, A:B1677 2i2t B2965 Oph·Pout A:B1156(OP2) B3308, B3309, B3310, B3311, B3312 A:B1155 G:B1157, C:B998 2i2t B2948 Oph·Pout U:B120(OP2) B3228, B3229, B3230, B3231, B3232 G:B121 G:B123, G:B121, G:B122 2i2t B2969 Oph·Pout A:B1664(OP2) B3327, B3328, B3329, B3330, B3331 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666 2i2t B2930 Oph·Pout A:B945(OP1) B3145, B3146, B3147, B3148, B3149 G:B831 G:B831, U:B832 2i2t B2949 Oph·Pout U:B120(OP1) B3233, B3234, B3235, B3236, B3237 G:B123 G:B123, G:B124 2i2u A1578 Oph·Pout C:A934(OP1) A1766, A1767, A1768, A1769, A1770 U:A1345 U:A1345 2i2u A1592 Oph·Pout A:A1110(OP2) A1838, A1839, A1840, A1841, A1842 C:A1109 A:A1111 2i2u A1561 Oph·Pout A:A1433(OP2) A1686, A1687, A1688, A1689, A1690 A:A1434 A:A1434, G:A1435 2i2u A1568 Oph·Pout G:A100(OP2) A1717, A1718, A1719, A1720, A1721 A:A101 G:A64, A:A101, G:A102 2i2u A1565 Oph·Pout A:A608(OP2) A1704, A1705, A1706, A1707, A1708 A:A609 A:A630, A:A609, C:A631, U:A610 2i2u A1573 Oph·Pout C:A352(OP2) A1740, A1741, A1742, A1743, A1744 G:A354 C:A330, C:A352, G:A331 C:A330, G:A354, A:A59 2i2u A1558 Oph·Pout G:A21(OP1) A1673, A1674, A1675, A1676, A1677 U:A561 G:A568, G:A567 A:A573, G:A567 2i2u A1595 Oph·Pout U:A1224(OP1) A1851, A1852, A1853, A1854, A1855 G:A951 C:A1223 C:A1223, A:A977, A:A974 2i2v B2949 Oph·Pout G:B297(OP2) B3239, B3240, B3241, B3242, B3243 G:B338 G:B298 2i2v B2926 Oph·Pout A:B1156(OP2) B3129, B3130, B3131, B3132, B3133 A:B1155 U:B999, G:B1157, C:B998 2i2v B3009 Oph·Pout A:B1676(OP2) B3495, B3496, B3497, B3498, B3499 C:B1675 A:B1676, A:B1677 2i2v B2931 Oph·Pout A:B945(OP1) B3156, B3157, B3158, B3159, B3160 G:B831 G:B831, U:B832 2i2v B2961 Oph·Pout A:B621(OP2) B3296, B3297, B3298, L798 G:B622 2i2v B2965 Oph·Pout U:B419(OP1) B3316, B3317, B3318, B3319, B3320 G:B230 G:B230 2i2v B2974 Oph·Pout U:B1313(OP1) B3361, B3362, B3363, B3364, B3365 G:B1334 2i2v B2924 Oph·Pout G:B2502(OP2) B3121, B3122, B3123, B3124 G:B2446 G:B2061, C:B2501, A:B2060 A:B2060, G:B2445, G:B2446 2i2v B2913 Oph·Pout A:B1664(OP2) B3067, B3068, B3069, B3070, B3071 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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