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

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Representative site 2z4k:A1546, See in JSmolMgRNA representative site for type PO-2BO         Click on the image to toggle views

Site type: Pout·2Bout

Schematic drawing for

MgRNA type PO-2BO
List of all 343 Mg2+ binding sites with the site type Pout·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
1egk C3 Pout·2Bout B61, C28, C29, C30, C31, C32 DA:B45 A:C104, G:C105
1ehz A570 Pout·2Bout A731, A732, A733, A734, A735, A736 C:A25 U:A41, G:A42
1evv A904 Pout·2Bout A936, A937, A938, A939, A940, A941 C:A25 G:A42, U:A41
1vs5 A1557 Pout·2Bout A1666, A1667, A1668, A1669, A1670, A1671 A:A1046 G:A1047, G:A1048
1vs5 A1564 Pout·2Bout A1702, A1703, A1704, A1705, A1706, A1707 A:A781 G:A799, G:A800
1vs6 B2997 Pout·2Bout B3438, B3439, B3440, B3441, B3442, B3443 U:B686 G:B770, G:B771
1vs7 A1562 Pout·2Bout A1689, A1690, A1691, A1692, A1693, A1694 G:A1079 G:A1077, U:A1076
1vs7 A1564 Pout·2Bout A1701, A1702, A1703, A1704, A1705, A1706 A:A315 G:A319, G:A318
1vt2 A3002 Pout·2Bout A3503, A3504, A3505, A3506, A3507, A3508 C:A2616 G:A2049, C:A2047
1y26 X101 Pout·2Bout X267, X268, X269, X270, X271, X272 A:X45 G:X46, U:X47
1yls B244 Pout·2Bout B367, B368, B369, B370, B371, B372 U:B212 G:B213, U:B231
2avy A1562 Pout·2Bout A1693, A1694, A1695, A1696, A1697, A1698 G:A266 G:A257, G:A258
2avy A1556 Pout·2Bout A1665, A1666, A1667, A1668, A1669, A1670 A:A1046 G:A1047, G:A1048
2aw7 A1563 Pout·2Bout A1702, A1703, A1704, A1705, A1706, A1707 A:A315 G:A319, G:A318
2aw7 A1561 Pout·2Bout A1690, A1691, A1692, A1693, A1694, A1695 G:A1079 G:A1077, U:A1076
2i2p A1545 Pout·2Bout A1614, A1615, A1616, A1617, A1618, A1619 G:A803 G:A771, U:A772
2i2t B3018 Pout·2Bout B3531, B3532, B3533, B3534, B3535, B3536 G:B2597 G:B2595, U:B1971
2i2t B3019 Pout·2Bout B3538, B3539, B3540, 4754, 4756, 4759 A:B2740 G:B2742, U:B2743
2i2v B2957 Pout·2Bout B3276, B3277, B3278, B3279, B3280, B3281 A:B2386 C:B2326, A:B2386
2i2v B2917 Pout·2Bout B3085, B3086, B3087, B3088, B3089, B3090 A:B2033 G:B2027, U:B2028
2i2v B2969 Pout·2Bout B3337, B3338, B3339, B3340, B3341, B3342 G:B649 C:B650, G:B651
2i2v B3018 Pout·2Bout B3530, B3531, B3532, B3533, B3534, B3535 G:B2597 G:B2595, U:B1971
2otj 08100 Pout·2Bout 03788, 04283, 05543, 06186, 07847 C:02077 G:02079, G:02080
2qal A2077 Pout·2Bout A2078, A2079, A2080, A2081, A2082, A2083 A:A1046 G:A1047, G:A1048
2qan A2134 Pout·2Bout A2135, A2136, A2137, A2138, A2139, A2140 A:A1046 G:A1047, G:A1048

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>