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

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Representative site 2qbb:A2049, See in JSmolMgRNA representative site for type 2PO-BO         Click on the image to toggle views

Site type: 2Pout·Bout

Schematic drawing for

MgRNA type 2PO-BO
List of all 169 Mg2+ binding sites with the site type 2Pout·Bout 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
1egk A24 2Pout·Bout A40, A41, A42, A43, A44, A45 A:A19, DC:D153 A:A19
1vs5 A1566 2Pout·Bout A1711, A1712, A1713, A1714, A1715, A1716 A:A729, G:A727 G:A727
1vs7 A1570 2Pout·Bout A1734, A1735, A1736, A1737, A1738, A1739 C:A726, G:A727 G:A727
1vs8 N128 2Pout·Bout B3286, B3287, B3288, N391, N394, N396 G:B1653, A:B2820 G:B2822
2avy A1550 2Pout·Bout A1638, A1639, A1640, A1641, A1642, A1643 A:A329, A:A315 G:A319
2aw4 B2997 2Pout·Bout B3434, B3435, B3436, B3437, B3438, B3439 U:B686, C:B687 G:B770
2awb N128 2Pout·Bout B3289, B3290, B3291, N391, N394, N396 G:B1653, A:B2820 G:B2822
2awb B2959 2Pout·Bout B3277, B3278, B3279, B3280, B3281, Q381 A:B582, A:B1253 C:B584
2i2u A1586 2Pout·Bout A1811, A1812, A1813, A1814, A1815, A1816 G:A1356, A:A1357 C:A1359
2i2u A1582 2Pout·Bout A1788, A1789, A1790, A1791, A1792, A1793 A:A1046, G:A1047 G:A1047
2qal A2328 2Pout·Bout A2329, A2330, A2331, A2332, A2333, A2334 A:A1394, A:A918 A:A919
2qal A2231 2Pout·Bout A2232, A2234, A2235, A2236, T2233 U:A323, G:A324 G:A324
2qal A2143 2Pout·Bout A2144, A2145, A2146, A2147, A2148, A2149 A:A1357, G:A1356 C:A1359
2qao B3337 2Pout·Bout B3895, B3896, B3897, B3898, B3899, B3900 G:B1653, G:B2819 A:B2821
2qb9 A2007 2Pout·Bout A2364, A2365, A2366, A2367, A2368, A2369 G:A1079, G:A1077 G:A1077
2qb9 A2143 2Pout·Bout A2472, A2473, A2474, A2475, A2476, A2477 A:A1357, G:A1356 C:A1359
2qba B3521 2Pout·Bout B4032, B4033, B4034, B4035, B4036, B4037 U:B769, G:B770 G:B770
2qbb A2353 2Pout·Bout A2659, A2660, A2661, A2662, A2663, A2664 G:A259, G:A258 G:A259
2qbb A2049 2Pout·Bout A2410, A2411, A2412, A2413, A2414, A2415 A:A171, A:A172 G:A148
2qbf E167 2Pout·Bout A1728, A1729, A1730, A1731, A1732 U:A20, G:A21 G:A21
2qbf A1601 2Pout·Bout T358, A1892, A1893, A1894, A1895, A1896 G:A259, G:A258 G:A259
2qbh A1566 2Pout·Bout A1713, A1714, A1715, A1716, A1717, A1718 A:A1357, G:A1356 C:A1359
2qbi B2997 2Pout·Bout B3433, B3434, B3435, B3436, B3437, B3438 U:B769, G:B770 G:B770
2qbj A1551 2Pout·Bout A1644, A1645, A1646, A1647, A1648, A1649 A:A171, A:A172 G:A148
2qou A1550 2Pout·Bout A1933, A1934, A1935, A1936, A1937, A1938 C:A316, A:A315 G:A319

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>