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

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Representative site 2qal:A2335, See in JSmolMgRNA representative site for type RO-3BO         Click on the image to toggle views

Site type: Rout·3Bout

Schematic drawing for

MgRNA type RO-3BO
List of all 13 Mg2+ binding sites with the site type Rout·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
2avy A1598 Rout·3Bout A1868, A1869, A1870, A1871, A1872, A1873 C:A1399 G:A926, G:A1505, C:A1399
2i2u A1583 Rout·3Bout A1794, A1795, A1796, A1797, A1798, A1799 A:A1362 G:A976, G:A1361, A:A1362
2qal A2335 Rout·3Bout A2336, A2337, A2338, A2339, A2340, A2341 C:A1399 G:A1505, C:A1399, G:A926
2qox B2939 Rout·3Bout B3185, B3186, B3187, B3188, B3189, B3190 A:B447 G:B473, C:B31, G:B474
2qoy A1557 Rout·3Bout A1967, A1968, A1969, A1970, A1971, A1972 C:A1359 C:A979, A:A1360, C:A980
3df1 A2335 Rout·3Bout A4336, A4337, A4338, A4339, A4340, A4341 C:A1399 C:A1399, G:A1401, G:A1505
3oas A2991 Rout·3Bout A3453, A3454, A3455, A3456, A3457, A3458 G:A976 G:A977, G:A978, G:A976
3ofc A2983 Rout·3Bout A3412, A3413, A3414, A3415, A3416, A3417 A:A2054 U:A2034, G:A2035, A:A574
3orb A2983 Rout·3Bout A3411, A3412, A3413, A3414, A3415, A3416 A:A2054 U:A2034, G:A2035, A:A574
3v27 A3495 Rout·3Bout A4621, A4622, A4623, A4624, A4625 G:A1904 G:A1840, G:A1839, A:A1927
3v27 A3503 Rout·3Bout A4656, A4657, A4658, A4659, A4660, A4661 G:A739 G:A741, G:A742, U:A740
3v2d A3167 Rout·3Bout A4157, A4158, A4159, A4160, A4161 U:A1142 G:A1015, G:A1016, G:A1017
4qcp A3604 Rout·3Bout A4897, A4898, A4899, A4900, A4901, A4902 U:A395 G:A397, G:A398, G:A396

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>