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

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Representative site 2qan:A2016, See in JSmolMgRNA representative site for type 2PO-2BO        Click on the image to toggle views

Site type: 2Pout·2Bout

Schematic drawing for

MgRNA type 2PO-2BO
List of all 279 Mg2+ binding sites with the site type 2Pout·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"
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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
1vs5 A1600 2Pout·2Bout A1878, A1879, A1880, A1881, A1882, A1883 G:A258, G:A259 G:A259, G:A260
1vs6 B2957 2Pout·2Bout B3266, B3267, B3268, B3269, B3270, B3271 A:B616, G:B617 G:B617, G:B618
1vs6 B3001 2Pout·2Bout B3456, B3457, B3458, B3459, B3460, B3461 A:B1000, A:B1001 G:B1003, G:B1002
1vs6 B2937 2Pout·2Bout B3174, B3175, B3176, B3177, B3178, B3179 G:B649, C:B650 C:B650, G:B651
1vs7 A1566 2Pout·2Bout A1712, A1713, A1714, A1715, A1716, A1717 A:A1046, G:A1047 G:A1048, G:A1047
1vs8 B2907 2Pout·2Bout B3025, B3026, B3027, B3028, B3029, B3030 G:B831, U:B568 A:B945, A:B2448
1vt2 A2921 2Pout·2Bout A3127, A3128, A3129, A3130, A3131, A3132 A:A616, A:A608 G:A618, G:A619
1yjn 08100 2Pout·2Bout 03782, 04270, 05525, 06169, 07837, 07838 U:02078, C:02077 G:02079, G:02080
1yls B242 2Pout·2Bout B355, B356, B357, B358, B359, B360 C:B215, G:B216 G:B216, G:B217
2avy A1599 2Pout·2Bout A1874, A1875, A1876, A1877, A1878, A1879 G:A258, G:A259 G:A259, G:A260
2aw4 B2937 2Pout·2Bout B3171, B3172, B3173, B3174, B3175, B3176 G:B649, C:B650 C:B650, G:B651
2aw4 B3001 2Pout·2Bout B3452, B3453, B3454, B3455, B3456, B3457 A:B1000, A:B1001 G:B1003, G:B1002
2aw7 A1565 2Pout·2Bout A1713, A1714, A1715, A1716, A1717, A1718 A:A1046, G:A1047 G:A1048, G:A1047
2i2p A1598 2Pout·2Bout A1871, A1872, A1873, A1874, A1875, A1876 A:A918, A:A1394 A:A918, A:A919
2i2p A1550 2Pout·2Bout A1639, A1640, A1641, A1642, A1643, A1644 A:A315, U:A317 G:A318, G:A319
2i2u A1581 2Pout·2Bout A1778, A1779, A1780, A1781, A1782 A:A937, C:A936 C:A1344, G:A1343
2i2v B3020 2Pout·2Bout B3537, B3538, B3539, B3540, B3541, 41054 A:B2741, A:B2740 G:B2742, U:B2743
2i2v B3016 2Pout·2Bout B3523, B3524, B3525, B3526, C1034, C1036 A:B1791, C:B1790 U:B1827, G:B1828
2qal A2342 2Pout·2Bout A2343, A2344, A2345, A2346, A2347, A2348 G:A259, G:A258 G:A259, G:A260
2qal A2014 2Pout·2Bout A2015, A2016, A2017, A2018, A2019, A2020 U:A804, G:A803 U:A772, G:A771
2qam B3543 2Pout·2Bout B4053, B4054, B4055, B4056, B4057, B4058 A:B1000, A:B1001 G:B1003, G:B1002
2qam B3521 2Pout·2Bout B4035, B4036, B4037, B4038, B4039, B4040 U:B686, C:B687 G:B771, G:B770
2qan A2121 2Pout·2Bout A2122, A2123, A2124, A2125, A2126, A2127 A:A315, U:A317 G:A319, G:A318
2qan A2016 2Pout·2Bout A2017, A2018, A2019, A2020, A2021, A2022 G:A803, U:A804 G:A771, U:A772
2qan A2340 2Pout·2Bout A2341, A2342, A2343, A2344, A2345 C:A110, G:A111 G:A111, G:A112

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>