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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 8 of 23 | | | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qp0 A1570 2Bout A2022, A2023, A2024, A2025, A2026, A2027 G:A1525, G:A1526
2qp1 B2933 2Bout B3662, B3663, B3664, B3665, B3666, B3667 G:B797, G:B798
2qp1 B2952 2Bout B3749, B3750, B3751, B3752, B3753, B3754 G:B2549, G:B2550
2r1s A17 2Bout A23, A30, A54, A65, A68, A93 G:A12, C:A11
2r20 A17 2Bout A23, A30, A53, A64, A67, A90 G:A12, C:A11
2z4k A1593 2Bout A1841, A1842, A1843, A1844, A1845, A1846 U:A37, G:A38
2z4k A1589 2Bout A1821, A1822, A1823, A1824, A1825, A1826 G:A1526, G:A1525
2z4k A1569 2Bout A1730, A1731, A1732, A1733, A1734, A1735 G:A941, G:A942
2z4k A1575 2Bout A1759, A1760, A1761, A1762, A1763, A1764 G:A1385, G:A1386
2z4l B2962 2Bout B3282, B3283, B3284, B3285, B3286, B3287 G:B797, G:B798
2z4l B2985 2Bout B3392, B3393, B3394, B3395, B3396, B3397 G:B2549, G:B2550
2z4l B2925 2Bout B3108, B3109, B3110, B3111, B3112, B3113 A:B756, G:B757
2z4m A1595 2Bout A1856, A1857, A1858, A1859, A1860, A1861 U:A37, G:A38
2z4m A1562 2Bout A1689, A1690, A1691, E168, E169, E170 U:A1076, G:A1077
2z4m A1571 2Bout A1743, A1744, A1745, A1746, A1747, A1748 G:A377, G:A376
2z4n B2971 2Bout B3336, B3337, B3338, B3339, B3340, B3341 G:B651, U:B652
2z4n B2972 2Bout B3342, B3343, B3344, B3345, B3346, B3347 G:B757, A:B756
2z4n B2934 2Bout B3158, B3159, B3160, B3161, B3162, B3163 G:B797, G:B798
2z4n B2970 2Bout B3330, B3331, B3332, B3333, B3334, B3335 G:B1259, U:B580
3cc2 08063 2Bout 03740, 06577, 07007, 07324, 07400, 07453 G:01364, G:01363
3df1 A2157 2Bout A4158, A4159, A4160, A4161, A4162, A4163 G:A941, G:A942
3df1 A2192 2Bout A4193, A4194, A4195, A4196, A4197, A4198 G:A1385, G:A1386
3df1 A2270 2Bout A4271, A4272, A4273, A4274, A4275, A4276 G:A1525, G:A1526
3df2 B3117 2Bout B4118, B4119, B4120, B4121, B4122, B4123 A:B739, G:B757
3df2 B3331 2Bout B4333, B4336, E4332, E4334, E4335, E4337 G:B797, G:B798

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>