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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
4Pout

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"
Page 1 of 7 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3l0u A77 4Pout A80, A81, A82, A83, A84, A85 U:A8, A:A9, C:A11, U:A12
4tra A79 4Pout A193, A194, A195, A196, A197, A198 U:A12, U:A8, A:A9, C:A11
6tna A79 4Pout A154, A155, A156, A157, A158, A159 U:A12, U:A8, A:A9, C:A11
3ofx N101 4Pout A1654, A1655, A1656, A1657, A1658, N106 U:A1049, C:A1203, A:A1204, G:A1048
3ofa N101 4Pout A1654, A1655, A1656, A1657, A1658, N106 U:A1049, C:A1203, A:A1204, G:A1048
3ofo N102 4Pout A1653, A1654, A1655, N103, N106, N109 U:A1049, C:A1203, G:A1048, A:A1204
3owi A107 4Pout A150, A151, A152, A153, A154, B134 G:A32, U:A67, C:A68, G:B10
3oxj A107 4Pout A132, A133, A134, A135, A136, B125 G:A32, U:A67, C:A68, G:B10
3oww B108 4Pout A154, B135, B136, B137, B138, B139 G:A10, U:B67, G:B32, C:B68
3owi B108 4Pout B135, B136, B137, B138, B139, B140 G:A10, U:B67, G:B32, C:B68
3oxe B134 4Pout A149, B142, B143, B144, B145, B146 G:A10, U:B67, G:B32, C:B68
3hhn C151 4Pout C150, C152, C153, C154, C155, C156 A:C95, A:C96, U:C94, G:C118
3hhn E191 4Pout E190, E192, E193, E194, E195, E196 A:E102, C:E101, C:E83, U:E84
4tp4 N201 4Pout A1779, A1780, A1781, N304, N305, N306 A:A1204, G:A1048, U:A1049, C:A1203
4tp0 N201 4Pout A1781, A1782, A1783, A1784, N302, N303 U:A1049, C:A1203, A:A1204, G:A1048
1yls D247 4Pout B384, B385, B386, B387, B388, D383 C:B235, G:D236, G:B236, C:D235
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
3i1o A1547 4Pout A1652, A1653, A1654, A1655, A1656, N130 A:A1204, G:A1048, U:A1049, C:A1203
2aw7 A1548 4Pout A1628, A1629, A1630, A1631, A1632, A1633 A:A16, U:A13, U:A14, G:A15
2qbj A1548 4Pout A1628, A1629, A1630, A1631, A1632, A1633 U:A13, U:A14, A:A16, G:A15
1vs7 A1549 4Pout A1629, A1630, A1631, A1632, A1633, A1634 A:A16, U:A13, U:A14, G:A15
2aw7 A1550 4Pout A1638, A1639, A1640, A1641, A1642, A1643 G:A350, C:A334, U:A333, A:A349
3oar A1550 4Pout A1651, A1652, A1653, A1654, A1655, N105 A:A1204, G:A1048, U:A1049, C:A1203

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