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

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
1dfu M501 Ob U:M95(O4) M518, M525, M529, N520, P131 A:M94, G:M96, U:N80
1f27 A35 Ob U:A7(O4) A162, A164, A173 G:A6
1ffy T1204 Ob G:T43(O6) T1218, T1308, T1309, T1310, T1311 U:T42, G:T26, A:T44
1hr2 A11 Ob G:A188(O6) A342, A343, A344, A345, A346 U:A168, U:A182, C:A166, A:A183, C:A165 A:A183
1hr2 B12 Ob G:B188(O6) B346, B347, B348, B349, B350 U:B182, U:B168, A:B183, C:B166, C:B165 A:B183
1m90 A8053 Ob G:A471(O6) A3936, A5159, A8725, A8763, A9561 A:A882 G:A469, U:A888, C:A881 U:A470, U:A883
1qu2 T1204 Ob G:T43(O6) T1218, T1308, T1309, T1310, T1311 U:T42, G:T26, A:T44
1vs5 A1562 Ob G:A1050(O6) A1691, A1692, A1693, A1694, A1695 G:A1207, C:A1051, G:A1048
1vs5 A1601 Ob U:A1358(O4) A1884, A1885, A1886, A1887, A1888 A:A1357 C:A1359, A:A1357, G:A976
1vs5 A1602 Ob G:A1417(O6) A1889, A1890, A1891, A1892, A1893 G:A1416, G:A1415 G:A1482, G:A1416
1vs5 A1576 Ob G:A1370(O6) A1762, A1763, A1764, A1765, A1766 G:A1371, U:A1351, C:A1352
1vs6 B2936 Ob U:B746(O4) B3169, B3170, B3171, B3172, B3173 U:B744, C:B2611, C:B2610 G:B745
1vs6 B2946 Ob G:B2304(O6) B3211, B3212, B3213, B3214, B3215 G:B2303
1vs6 B2939 Ob C:B2499(O2) B3184, B3185, B3186, B3187, B3188 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
1vs7 A1580 Ob G:A1370(O6) A1787, A1788, A1789, A1790, A1791 U:A1351, G:A1371
1vs7 A1605 Ob G:A1417(O6) A1901, A1902, A1903, A1904, A1905 G:A1416, G:A1415 G:A1482, G:A1416
1vs8 B2970 Ob U:B746(O4) B3339, B3340, B3341, B3342, B3343 U:B744, C:B2610, C:B2611
1vs8 B2962 Ob G:B2304(O6) B3295, B3296, B3297, B3298, B3299 A:B2311, C:B2310
1vt2 A3014 Ob U:A1602(O4) A3544, A3545, A3546, T640 G:A1601, C:A1600, A:A1342
1vt2 A3032 Ob U:A2593(O4) A3620, A3621, A3622, A3623, C739 G:A2592 G:A2592, C:A2594
1vt2 A2926 Ob U:A746(O4) A3152, A3153, A3154, A3155, D210 U:A744, C:A2611, C:A2610
1vt2 A3000 Ob U:A2419(O4) A3496, A3497, A3498, 3568, 3571
2a43 A201 Ob G:A6(O6) A202, A203, A204, A205, A206 C:A10, G:A11 C:A7, G:A5
2avy A1561 Ob G:A1050(O6) A1688, A1689, A1690, A1691, A1692 G:A1207, C:A1051, G:A1048
2avy A1601 Ob G:A1417(O6) A1885, A1886, A1887, A1888, A1889 G:A1416, G:A1415 G:A1416, G:A1482

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>