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

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Representative site 2avy:A1578, See in JSmolMgRNA representative site for type PO-RO          Click on the image to toggle views

Site type: Pout·Rout

Schematic drawing for

MgRNA type PO-RO
List of all 37 Mg2+ binding sites with the site type Pout·Rout 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
1dno B23 Pout·Rout B209, B210, B211, B212, B213, B214 DC:B20 DC:B20
1jj2 A8065 Pout·Rout 03497, 09450, A8523, A8552, A8603, A8633 C:0783 G:0782
1k73 C8065 Pout·Rout A3966, A9924, C8521, C8551, C8603, C8634 C:A783 G:A782
1k9m C8065 Pout·Rout A3961, A9912, C8522, C8552, C8604, C8633 C:A783 G:A782
1m90 C8065 Pout·Rout A3496, A9444, C8525, C8551, C8598, C8626 C:A783 G:A782
1nji C8065 Pout·Rout A3960, A9920, C8523, C8549, C8601, C8631 C:A783 G:A782
1s72 A8065 Pout·Rout 03492, 09447, A8523, A8552, A8604, A8634 C:0783 G:0782
1vq5 A8065 Pout·Rout 03248, 04282, A9320, A9344, A9395, A9424 C:0783 G:0782
1vq7 A8065 Pout·Rout 03248, 04294, A9320, A9350, A9397, A9426 C:0783 G:0782
1yij A8065 Pout·Rout 03980, 09933, A8820, A8846, A8898, A8927 C:0783 G:0782
2avy A1578 Pout·Rout A1772, A1773, A1774, A1775, A1776, A1777 U:A916 U:A13
2otl A8065 Pout·Rout 03981, 09933, A8718, A8750, A8796, A8826 C:0783 G:0782
3cc2 A8065 Pout·Rout 03524, 09468, A8521, A8547, A8594, A8624 C:0783 G:0782
3cc7 A8050 Pout·Rout 04012, 09962, A8987, A9013, A9055, A9087 C:0783 G:0782
3i1p A2918 Pout·Rout A3112, A3113, A3114, A3115, A3116, A3117 G:A1256 U:A1255
3i1s A1570 Pout·Rout A1761, A1762, A1763, A1764, A1765 C:A503 C:A522
3i1t A2918 Pout·Rout A3111, A3112, A3113, A3114, A3115, A3116 G:A1256 U:A1255
3v27 A3619 Pout·Rout A5171, A5172, A5173, A5174, A5175, A5176 G:A680 G:A189
3v28 A1754 Pout·Rout A2031, A2032, A2033, L201, L202 G:A537 C:A503
3v2c A1642 Pout·Rout A1934, A1935, A1936, A1937 C:A934 U:A1345
4a1a 08 Pout·Rout 05059, 05060, 05061, 05062, 05063, 05064 C:238 G:236
4bpe A5007 Pout·Rout A2001, A2128, A2129, A2251, A2345, A2346 A:A600 C:A4
4bpn A5052 Pout·Rout A6173, A6174, A6175, A6176, A6177, A6178 C:A672 A:A675
4bpn A5007 Pout·Rout A6102, A6109, A6116, A6123, A6130, A6137 A:A600 C:A4
4bpo A5007 Pout·Rout A2001, A2128, A2129, A2332, A2333, A2334 A:A600 C:A4

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>