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

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Representative site 2qoz:B2982, See in JSmolMgRNA representative site for type PO-3BO         Click on the image to toggle views

Site type: Pout·3Bout

Schematic drawing for

MgRNA type PO-3BO
List of all 341 Mg2+ binding sites with the site type Pout·3Bout 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 C9 Pout·3Bout B64, C64, C65, C67, C68, D63 G:C103 DG:B36, DA:B45, DG:D132
1egk A25 Pout·3Bout A46, A47, A48, B65, B66, D70 G:A3 DG:B32, DG:D136, DA:D135
1ffy T1202 Pout·3Bout T1298, T1299, T1300, T1301, T1302, T1303 A:T58 G:T53, U:T54, U:T55
1hr2 A16 Pout·3Bout A353, A354, A355, A356, A357, A358 A:A114 G:A116, U:A205, A:A115
1qu2 T1202 Pout·3Bout T1298, T1299, T1300, T1301, T1302, T1303 A:T58 G:T53, U:T54, U:T55
1vs5 A1563 Pout·3Bout A1696, A1697, A1698, A1699, A1700, A1701 G:A266 G:A257, G:A258, G:A259
1vs5 A1558 Pout·3Bout A1672, A1673, A1674, A1675, N142, N143 A:A1360 C:A980, G:A1361, A:A1360
1vs7 A1568 Pout·3Bout A1724, A1725, A1726, A1727, A1728, A1729 A:A781 U:A798, G:A800, G:A799
1vs7 A1567 Pout·3Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259
1vs7 A1559 Pout·3Bout A1677, A1678, A1679, A1680, N150 A:A1360 C:A980, G:A1361, A:A1360
1vs8 B2956 Pout·3Bout B3263, B3264, B3265, B3266, B3267, B3268 A:B2386 C:B2326, U:B2387, A:B2386
1vt2 A2992 Pout·3Bout A3457, A3458, A3459, A3460, A3461, A3462 G:A977 G:A977, G:A978, G:A976
1vt2 A3015 Pout·3Bout A3547, A3548, A3549, A3550, A3551, 2647 U:A686 G:A771, U:A769, G:A770
1yj9 08071 Pout·3Bout 03935, 05862, 07216, 07347, 07618 A:01815 U:01813, C:01818, U:01817
2avy A1557 Pout·3Bout A1671, A1672, N130, N131, N132, N135 A:A1360 C:A980, G:A1361, A:A1360
2avy A1563 Pout·3Bout A1699, A1700, A1701, A1702, A1703, A1704 A:A781 G:A799, G:A800, U:A798
2aw4 B2922 Pout·3Bout B3095, B3096, B3097, B3098, B3099, B3100 U:B1267 G:B2010, U:B2011, G:B2012
2aw7 A1558 Pout·3Bout A1678, A1679, A1680, A1681, N141 A:A1360 C:A980, A:A1360, G:A1361
2aw7 A1567 Pout·3Bout A1725, A1726, A1727, A1728, A1729, A1730 A:A781 G:A800, U:A798, G:A799
2aw7 A1566 Pout·3Bout A1719, A1720, A1721, A1722, A1723, A1724 G:A266 G:A257, G:A258, G:A259
2awb B2957 Pout·3Bout B3267, B3268, B3269, B3270, B3271, B3272 A:B2386 C:B2326, U:B2387, A:B2386
2gcs B505 Pout·3Bout B211, B300, B330, B331, B332, B333 A:B129 U:B100, G:B102, G:B101
2h0x B505 Pout·3Bout B211, B300, B330, B331, B332, B333 A:B129 U:B100, G:B102, G:B101
2i2p A1563 Pout·3Bout A1703, A1704, A1705, A1706, K165, K168 A:A781 G:A799, G:A800, U:A798
2i2p A1575 Pout·3Bout A1765, A1766, A1767, A1768, A1769 U:A1348 G:A1370, G:A1371, U:A1372

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>