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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"
Page 3 of 19 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qao B3351 Ob G:B2304(O6) B3907, B3908, B3909, B3910, B3911 C:B2310 U:B2302, G:B2303
2qao B3468 Ob C:B2499(O2) B4002, B4003, B4004, B4005, B4006 C:B2055, U:B2500, G:B2454, G:B2032
2qao B3403 Ob U:B746(O4) B3951, B3952, B3953, B3954, B3955 C:B2610, C:B2611, U:B744 G:B745
2qb9 A2355 Ob G:A1417(O6) A2647, A2648, A2649, A2650, A2651 G:A1416, G:A1415 G:A1416, G:A1482
2qb9 A2199 Ob G:A1370(O6) A2519, A2520, A2521, A2522, A2523 G:A1371, U:A1351
2qb9 A2109 Ob G:A1050(O6) A2446, A2447, A2448, A2449, A2450
2qba B3206 Ob C:B2499(O2) B3780, B3781, B3782, B3783, B3784 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qba B3188 Ob U:B746(O4) B3765, B3766, B3767, B3768, B3769 U:B744, C:B2610, C:B2611 G:B745
2qbb A2225 Ob G:A1370(O6) A2555, A2556, A2557, A2558, A2559 U:A1351, G:A1371
2qbb A2366 Ob G:A1417(O6) A2670, A2671, A2672, A2673, A2674 G:A1416, G:A1415 G:A1482, G:A1416
2qbc B3468 Ob C:B2499(O2) B4001, B4002, B4003, B4004, B4005 C:B2499 C:B2055, U:B2500, G:B2032, G:B2454
2qbd A2355 Ob G:A1417(O6) A2356, A2357, A2358, A2359, A2360 G:A1415 G:A1482, G:A1416
2qbd A2109 Ob G:A1050(O6) A2110, A2111, A2112, A2113, A2114 G:A1048, G:A1207, C:A1051
2qbd A2199 Ob G:A1370(O6) A2200, A2201, A2202, A2203, A2204 G:A1371, U:A1372, U:A1351
2qbe B3240 Ob G:B2304(O6) B3806, B3807, B3808, B3809, B3810 G:B2303, U:B2302
2qbe B3206 Ob C:B2499(O2) B3779, B3780, B3781, B3782, B3783 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454
2qbe B3188 Ob U:B746(O4) B3765, B3766, B3767, B3768, D210 C:B2610, C:B2611, U:B744 G:B745
2qbe B3418 Ob U:B2028(O4) B3950, B3951, B3952, B3953 A:B2033 G:B2029, G:B2027
2qbf A1603 Ob G:A1417(O6) A1902, A1903, A1904, A1905, A1906 G:A1415 G:A1482, G:A1415, G:A1416
2qbf A1578 Ob G:A1370(O6) A1787, A1788, A1789, A1790, A1791 G:A1371, U:A1372, U:A1351
2qbg B2984 Ob C:B2499(O2) B3399, B3400, B3401, B3402, B3403 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454
2qbg B2972 Ob U:B746(O4) B3350, B3351, B3352, B3353, D408 C:B2611, U:B744 G:B745
2qbg B2964 Ob G:B2304(O6) B3306, B3307, B3308, B3309, B3310 G:B2308 U:B2302, G:B2303
2qbh A1601 Ob U:A1358(O4) A1883, A1884, A1885, A1886, A1887 C:A1359, A:A1357
2qbh A1602 Ob G:A1417(O6) A1888, A1889, A1890, A1891, A1892 G:A1416, G:A1415 G:A1416, U:A1481, G:A1482

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>