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

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Representative site 2i2v:B2959, See in JSmolMgRNA representative site for type PO-RO-3BO      Click on the image to toggle views

Site type: Pout·Rout·3Bout

Schematic drawing for

MgRNA type PO-RO-3BO
List of all 32 Mg2+ binding sites with the site type Pout·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
1fuf A97 Pout·Rout·3Bout A92, A93, A96, B94, B95 U:A7 U:A6 U:B17, G:B15, G:B16
1vs5 A1599 Pout·Rout·3Bout A1872, A1873, A1874, A1875, A1876, A1877 C:A1400 C:A1399 G:A926, G:A1505, C:A1399
2i2v B2959 Pout·Rout·3Bout B3286, B3287, B3288, B3289, B3290, B3291 A:B582 C:B1251 C:B584, A:B582, G:B583
2qow A1546 Pout·Rout·3Bout A1896, A1897, A1898, A1899, A1900, A1901 G:A803 G:A803 U:A772, G:A773, G:A771
2qp1 B2957 Pout·Rout·3Bout B3773, B3774, B3775, B3776, B3777, B3778 A:B2386 U:B2384 C:B2326, U:B2387, A:B2386
2z4l B2983 Pout·Rout·3Bout B3380, B3381, B3382, B3383, B3384, B3385 A:B2386 U:B2384 C:B2326, A:B2386, U:B2387
3df1 A2219 Pout·Rout·3Bout A4220, A4221, A4222, A4223, A4224, A4225 U:A916 U:A13 U:A13, U:A916, G:A917
3i1r A2941 Pout·Rout·3Bout A3214, A3215, A3216, A3217, A3218, A3219 U:A1267 G:A1266 G:A2010, U:A2011, G:A2012
3oat A2982 Pout·Rout·3Bout A3399, A3400, A3401, A3402, A3403, A3404 C:A2055 A:A2054 U:A2034, G:A2035, A:A574
3oat A2940 Pout·Rout·3Bout A3206, A3207, A3208, A3209, A3210, A3211 U:A1267 G:A1266 G:A2010, U:A2011, G:A2012
3ofr A2984 Pout·Rout·3Bout A3409, A3410, A3411, A3412, A3413, A3414 C:A2055 A:A2054 U:A2034, G:A2035, A:A574
3ofz A2982 Pout·Rout·3Bout A3401, A3402, A3403, A3404, A3405, A3406 C:A2055 A:A2054 U:A2034, G:A2035, A:A574
3v27 A3573 Pout·Rout·3Bout A4976, A4977, A4978, A4979 U:A1955 G:A1954 G:A1950, G:A1948, G:A1949
3v27 A3597 Pout·Rout·3Bout A5056, A5057, A5058, A5059 G:A582 C:A1251 G:A582, G:A583, G:A585
4bpe A5001 Pout·Rout·3Bout A2148, A2149, A2161, A2162, A2163, A2245 G:A854 U:A913 G:A854, U:A913, A:A911
4bpn A5001 Pout·Rout·3Bout A6006, A6007, A6008, A6009, A6010, A6011 G:A854 U:A913 U:A913, G:A854, A:A911
4bpn A5025 Pout·Rout·3Bout A6433, A6434, A6435, A6436, A6437, A6438 C:A419 C:A416 G:A421, C:A416, A:A420
4bpo A5025 Pout·Rout·3Bout A2067, A2068, A2069, A2070, A2071, A2072 C:A419 C:A416 G:A421, C:A416, A:A420
4bpp A5001 Pout·Rout·3Bout A7027, A7028, A7029, A7030, A7031, A7032 G:A854 U:A913 U:A913, G:A854, A:A911
4dha A3742 Pout·Rout·3Bout A4879, A4880, A4881, A4882 U:A1955 G:A1954 G:A1948, G:A1949, G:A1950
4gar A3092 Pout·Rout·3Bout A3632, A3633, A3634, A3635 A:A1439 U:A1438 U:A1440, A:A1552, A:A1551
4gau A3078 Pout·Rout·3Bout A3572, A3573, A3574, A3575, A3576, A3577 U:A2034 A:A2054 G:A2035, A:A574, U:A2034
4nvw A3102 Pout·Rout·3Bout A4063, A4064, A4065, A4066 G:A21 G:A567 A:A573, A:A563, G:A567
4nvx A3294 Pout·Rout·3Bout A4147, A4148, A4149, A4150 C:A1333 U:A1313 U:A1335, G:A1334, U:A1316
4nw0 A3102 Pout·Rout·3Bout A4063, A4064, A4065, A4066 G:A21 G:A567 G:A567, A:A573, A:A563

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>