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

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Representative site 2qoy:A1567, See in JSmolMgRNA representative site for type 2BO            Click on the image to toggle views


Site type: 2Bout

Schematic drawing for
2Bout

MgRNA type 2BO
List of all 555 Mg2+ binding sites with the site type 2Bout 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 23 | | | 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
2qbe B3331 2Bout B3881, B3882, B3883, E203, E204, E205 G:B797, G:B798
2qbe B3246 2Bout B3811, B3812, B3813, B3814, B3815, B3816 U:B434, A:B42
2qbe B3117 2Bout B3707, B3708, B3709, B3710, B3711, B3712 A:B739, G:B757
2qbf A1577 2Bout A1781, A1782, A1783, A1784, A1785, A1786 G:A1386, G:A1385
2qbf A1570 2Bout A1745, A1746, A1747, A1748, A1749, A1750 G:A376, G:A377
2qbf A1594 2Bout A1858, A1859, A1860, A1861, A1862, A1863 G:A38, U:A37
2qbf A1565 2Bout A1710, A1711, A1712, A1713, A1714, A1715 G:A1048, G:A1047
2qbf A1561 2Bout E168, A1688, A1689, A1690, A1691, A1692 U:A1076, G:A1077
2qbg B2952 2Bout B3246, B3247, B3248, B3249, B3250, B3251 G:B2549, G:B2550
2qbg B2933 2Bout B3159, B3160, B3161, B3162, B3163, B3164 G:B797, G:B798
2qbg B2999 2Bout B3453, B3454, B3455, B3456, B3457, B3458 G:B770, G:B771
2qbg B2969 2Bout B3332, B3333, B3334, B3335, B3336, B3337 U:B580, G:B1259
2qbh A1592 2Bout A1837, A1838, A1839, A1840, A1841, A1842 G:A38, U:A37
2qbh A1574 2Bout A1754, A1755, A1756, A1757, A1758, A1759 G:A1385, G:A1386
2qbh A1579 2Bout A1776, A1777, A1778, A1779, A1780, A1781 G:A917, U:A916
2qbh A1588 2Bout A1817, A1818, A1819, A1820, A1821, A1822 G:A1525, G:A1526
2qbi B2961 2Bout B3281, B3282, B3283, B3284, B3285, E337 G:B798, G:B797
2qbi B2937 2Bout B3170, B3171, B3172, B3173, B3174, B3175 C:B650, G:B651
2qbi B2907 2Bout B3027, B3028, B3029, B3030, B3031, B3032 U:B580, G:B1259
2qbj A1590 2Bout A1835, A1836, A1837, A1838, A1839, A1840 G:A1526, G:A1525
2qbj A1577 2Bout A1779, A1780, A1781, A1782, A1783, A1784 G:A1386, G:A1385
2qbj A1570 2Bout A1743, A1744, A1745, A1746, A1747, A1748 G:A376, G:A377
2qbj A1594 2Bout A1855, A1856, A1857, A1858, A1859, A1860 U:A37, G:A38
2qbk B2952 2Bout B3242, B3243, B3244, B3245, B3246, B3247 G:B2549, G:B2550
2qbk B2970 2Bout B3333, B3334, B3335, B3336, B3337, B3338 G:B651, C:B650

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>