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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 2qox:B2986, See in JSmolMgRNA representative site for type 5PO            Click on the image to toggle views


Site type: 5Pout

Schematic drawing for
5Pout

MgRNA type 5PO
List of all 20 Mg2+ binding sites with the site type 5Pout 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4tol A1640 5Pout A1881, A1882, A1883, A1884, A1885, A1886 C:A503, C:A536, G:A537, C:A504, A:A523
4dv7 A1834 5Pout A2138, A2139, A2140, A2141, A2142, A2143 C:A330, C:A328, C:A314, A:A315, A:A329
3r8t A2958 5Pout A3326, A3327, A3328, A3329, A3330 A:A1772, A:A1773, G:A1828, G:A1972, G:A1973
2qox B2986 5Pout B3409, B3410, B3411, B3412, B3413, B3414 A:B2614, U:B2613, C:B2050, A:B2051, G:B2578
3i22 A2997 5Pout A3484, A3485, A3486, A3487, A3488, A3489 U:A1636, G:A1300, G:A1299, A:A1637, A:A1635
1vt2 A2998 5Pout A3485, A3486, A3487, A3488, A3489, A3490 U:A1636, G:A1300, G:A1299, A:A1637, A:A1635
4tp3 A3025 5Pout A3313, A3314, A3315, A3316 G:A2599, G:A784, G:A2588, A:A2589, C:A2440
4tpb A3025 5Pout A3314, A3315, A3316, A3317 G:A2599, G:A784, G:A2588, A:A2589, C:A2440
4tpf A3026 5Pout A3312, A3313, A3314, C303 G:A2599, G:A784, G:A2588, A:A2589, C:A2440
4too A3056 5Pout A3447, A3448, A3449, A3450, A3451 A:A1772, A:A1773, G:A1828, G:A1972, G:A1973
4tox A3057 5Pout A3450, A3451, A3452, A3453, A3454 A:A1772, A:A1773, G:A1828, G:A1972, G:A1973
4tp3 A3086 5Pout A3588, A3589, A3590, A3591, A3592 A:A981, C:A982, G:A977, G:A978, G:A561
4tpb A3086 5Pout A3588, A3589, A3590, A3591, A3592 A:A981, C:A982, G:A977, G:A978, G:A561
4pec A3101 5Pout A3665, A3666, A3667, A3668 G:A2056, G:A2057, U:A576, G:A577, A:A2503
4tp3 A3120 5Pout A3737, A3738, A3739, A3740 C:A192, A:A199, U:A2243, U:A193, C:A198
4tp7 A3121 5Pout A3736, A3737, A3738, A3739 C:A192, A:A199, U:A2243, U:A193, C:A198
4gar A3134 5Pout A3807, A3808, A3809, A3810, A3811, A3812 A:A2837, G:A2838, C:A2874, G:A2819, A:A2820
3v29 A3385 5Pout A3955, A3956, A3957, A3958, A3959, A3960 G:A738, C:A737, U:A1621, G:A1622, U:A767
3df4 B3485 5Pout B4486, B4487, B4488, B4489, B4490, B4491 U:B2613, C:B2050, A:B2614, A:B2051, G:B2578
3v2d A3650 5Pout A5501, A5502, A5503, A5504, A5505, A5506 G:A1606, G:A1303, A:A1608, C:A1304, C:A1607

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>