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

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Representative site 3df1:A2096, See in JSmolMgRNA representative site for type 4PO            Click on the image to toggle views

Site type: 4Pout

Schematic drawing for

MgRNA type 4PO
List of all 174 Mg2+ binding sites with the site type 4Pout 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
1ehz A560 4Pout A725, A726, A727, A728, A729, A730 U:A12, U:A8, A:A9, C:A11
1ffy T1201 4Pout T1292, T1293, T1294, T1295, T1296, T1297 U:T54, U:T55, A:T57, C:T56
1qu2 T1201 4Pout T1292, T1293, T1294, T1295, T1296, T1297 U:T54, U:T55, A:T57, C:T56
1vs5 A1560 4Pout A1680, A1681, A1682, A1683, A1684, A1685 A:A16, G:A15, U:A13, U:A14
1vs5 A1556 4Pout A1661, A1662, A1663, A1664, A1665, N130 A:A1204, G:A1048, U:A1049, C:A1203
1vs7 A1551 4Pout A1638, A1639, A1640, A1641, A1642, A1643 G:A350, C:A334, U:A333, A:A349
1vs7 A1549 4Pout A1629, A1630, A1631, A1632, A1633, A1634 A:A16, U:A13, U:A14, G:A15
1vs7 A1557 4Pout A1667, A1668, A1669, A1670, N135, N138 C:A1203, A:A1204, U:A1049, G:A1048
1yls D247 4Pout B384, B385, B386, B387, B388, D383 C:B235, G:D236, G:B236, C:D235
2avy A1559 4Pout A1677, A1678, A1679, A1680, A1681, A1682 A:A16, G:A15, U:A13, U:A14
2aw7 A1550 4Pout A1638, A1639, A1640, A1641, A1642, A1643 G:A350, C:A334, U:A333, A:A349
2aw7 A1556 4Pout A1667, A1668, A1669, A1670, A1671, N129 G:A1048, C:A1203, A:A1204, U:A1049
2aw7 A1548 4Pout A1628, A1629, A1630, A1631, A1632, A1633 A:A16, U:A13, U:A14, G:A15
2i2t B3004 4Pout B3475, B3476, B3477, B3478, B3479, B3480 U:B202, C:B383, C:B385, G:B205
2i2t B3022 4Pout B3550, B3551, B3552, B3553, B3554, N773 C:B2874, G:B2819, G:B2838, A:B2820
2i2t B2908 4Pout B3040, B3041, B3042, B3043, B3044, B3045 G:B559, C:B560, G:B2038, A:B1008
2i2v B3023 4Pout B3551, B3552, B3553, B3554, B3555, N1073 C:B2874, G:B2819, G:B2838, A:B2820
2i2v B2967 4Pout B3325, B3326, B3327, B3328, B3329, B3330 C:B560, G:B2038, G:B559, A:B1008
2otl 08072 4Pout 03241, 04009, 07413, 07817, 07874 U:0954, C:02298, G:02299, A:02301
2qal A2096 4Pout A2097, A2098, A2099, A2100, A2101, A2102 U:A13, U:A14, G:A15, A:A16
2qam B3382 4Pout B3923, B3924, B3925, B3926, B3927, B3928 A:B1669, C:B1986, A:B1987, C:B2551
2qan A2077 4Pout A2079, A2080, A2082, A2083, N2078, N2081 C:A1203, A:A1204, G:A1048, U:A1049
2qan A2029 4Pout A2030, A2031, A2032, A2033, A2034, A2035 A:A16, U:A14, U:A13, G:A15
2qan A2042 4Pout A2043, A2044, A2045, A2046, A2047, A2048 G:A350, C:A334, U:A333, A:A349
2qao B3344 4Pout B3901, B3902, B3903, B3904, B3905, B3906 U:B1915, A:B1912, A:B1913, A:B1916

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>