MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df1:A2096, See in JSmolClick on the image to toggle views Site type: 4Pout Schematic drawing for 4Pout List of all 174 Mg2+ binding sites with the site type 4Pout 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 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4pec A3055 4Pout A3447, A3448, A3449, A3450, A3451 A:A1772, A:A1773, G:A1828, G:A1972 4tp3 A3056 4Pout A3450, A3451, A3452, A3453, C302 A:A1772, G:A1973, G:A1828, G:A1972 4too A3057 4Pout A3452, A3453, A3454, A3455, A3456, A3457 G:A1959, A:A1937, C:A1958, A:A1936 4pec A3057 4Pout A3458, A3459, A3460, A3461 G:A1968, G:A2592, G:A1972, G:A1973 4too A3058 4Pout A3458, A3459, A3460, A3461 G:A1968, G:A2592, G:A1972, G:A1973 4tpf A3059 4Pout A3461, A3462, A3463, A3464 G:A1968, G:A2592, G:A1972, G:A1973 4tp7 A3059 4Pout A3458, A3459, A3460, A3461 G:A1968, G:A2592, G:A1972, G:A1973 4gar A3073 4Pout A3546, A3547, A3548, A3549, C405 G:A2588, A:A2589, A:A2587, A:A2600 4gar A3084 4Pout A3594, A3595, A3596, A3597, A3598 G:A561, G:A978, A:A981, C:A982 4too A3086 4Pout A3587, A3588, A3589, A3590, A3591 G:A561, G:A978, A:A981, C:A982 4tp7 A3087 4Pout A3588, A3589, A3590, A3591, A3592 A:A981, G:A977, G:A978, C:A982 4gau A3093 4Pout A3648, A3649, A3650, A3651, A3652 U:A1636, A:A1637, G:A1300, G:A1299 4too A3102 4Pout A3662, A3663, A3664, A3665 G:A2056, G:A2057, U:A576, A:A2503 4tox A3103 4Pout A3667, A3668, A3669, A3670 G:A2056, U:A576, A:A2503, G:A2057 4tp7 A3103 4Pout A3664, A3665, A3666, A3667 G:A2056, U:A576, A:A2503, G:A2057 4gau A3133 4Pout A3814, A3815, A3816, A3817, A3818, N201 G:A2819, C:A2874, G:A2838, A:A2820 4peb A3136 4Pout A3807, A3808, A3809, A3810, A3811, N204 G:A2819, C:A2874, G:A2838, A:A2820 4qcu A3161 4Pout A4118, A4119, A4120, A4121, A4122, A4123 U:A13, U:A14, G:A15, A:A16 4qcq A3168 4Pout A4148, A4149, A4150, A4151, A4152, A4153 U:A13, U:A14, G:A15, A:A16 4gar A3169 4Pout A3238, A3239, A3240, A3241, A3242 A:A449, G:A450, G:A452, A:A453 4qcy A3181 4Pout A4121, A4122, A4123, A4124, A4125, A4126 U:A13, U:A14, G:A15, A:A16 4nvy A3192 4Pout A4104, A4105, A4106, A4107, A4108, A4109 U:A13, U:A14, A:A16, G:A15 4nvu A3192 4Pout A4104, A4105, A4106, A4107, A4108, A4109 U:A13, U:A14, G:A15, A:A16 3v2f A3204 4Pout A3935, A3936, A3937, E404 U:A2580, G:A2581, G:A743, G:A744 3v23 A3325 4Pout A3980, A3981, A3982, A3983, A3984 C:A1611, C:A1617, A:A1610, C:A1615

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].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>