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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3i20:A2925, See in JSmolMgRNA representative site for type OB Click on the image to toggle views


Site type: Ob

Schematic drawing for
Ob
MgRNA type OB
List of all 468 Mg2+ binding sites with the site type Ob 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 A1561 Ob G:A1050(O6) A1688, A1689, A1690, A1691, A1692 G:A1207, C:A1051, G:A1048
2avy A1600 Ob U:A1358(O4) A1880, A1881, A1882, A1883, A1884 A:A1357 A:A1357, G:A976, C:A1359
2aw4 B2939 Ob C:B2499(O2) B3180, B3181, B3182, B3183, B3184 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2aw4 B2946 Ob G:B2304(O6) B3207, B3208, B3209, B3210, B3211 G:B2303
2aw7 A1579 Ob G:A1370(O6) A1789, A1790, A1791, A1792, A1793 U:A1351, G:A1371
2aw7 A1604 Ob G:A1417(O6) A1904, A1905, A1906, A1907, A1908 G:A1416, G:A1415 U:A1481, G:A1482, G:A1416
2awb B2971 Ob U:B746(O4) B3340, B3341, B3342, B3343, B3344 U:B744, C:B2610, C:B2611
2awb B2963 Ob G:B2304(O6) B3298, B3299, B3300, B3301, B3302 C:B2310
2i2p A1601 Ob G:A1417(O6) A1890, A1891, A1892, A1893, A1894 G:A1416, G:A1482
2i2t B3017 Ob U:B2593(O4) B3527, B3528, B3529, B3530, C280 G:B2592 C:B2594, G:B2599, G:B2592
2i2t B2936 Ob U:B746(O4) B3175, B3176, B3177, B3178, B3179 C:B2610, C:B2611, U:B744 G:B745
2i2t B2946 Ob G:B2304(O6) B3217, B3218, B3219, B3220, B3221 A:B2311, C:B2310 U:B2302, G:B2303
2i2t B2939 Ob C:B2499(O2) B3190, B3191, B3192, B3193, B3194 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454
2i2u A1594 Ob G:A1108(O6) A1847, A1848, A1849, A1850 U:A1095, C:A1096 G:A1094
2i2u A1576 Ob G:A1417(O6) A1755, A1756, A1757, A1758, A1759 G:A1416, G:A1415 G:A1482, G:A1415, G:A1416
2i2v B2983 Ob C:B2499(O2) B3401, B3402, B3403, B3404, B3405 G:B2032 C:B2055, U:B2500, G:B2454, G:B2032
2i2v B3017 Ob U:B2593(O4) B3527, B3528, B3529, C1039, C1041 G:B2592, C:B2591 G:B2592, G:B2599
2i2v B2963 Ob G:B2304(O6) B3305, B3306, B3307, B3308, B3309 C:B2310 U:B2302
2i2v B2971 Ob U:B746(O4) B3349, B3350, B3351, B3352, D854 C:B2610, C:B2611, U:B744 G:B745
2qal A2355 Ob G:A1417(O6) A2356, A2357, A2358, A2359, A2360 G:A1416, G:A1415 G:A1416
2qal A2199 Ob G:A1370(O6) A2200, A2201, A2202, A2203, A2204 G:A1371, U:A1351, C:A1352
2qam B3206 Ob C:B2499(O2) B3778, B3779, B3780, B3781, B3782 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454
2qam B3188 Ob U:B746(O4) B3764, B3765, B3766, B3767, B3768 C:B2610, C:B2611, U:B744 G:B745
2qan A2225 Ob G:A1370(O6) A2226, A2227, A2228, A2229, A2230 U:A1351, G:A1371
2qan A2366 Ob G:A1417(O6) A2367, A2368, A2369, A2370, A2371 G:A1416, G:A1415 G:A1482, G:A1416

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>