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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 4 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
2qbh A1586 Ob G:A1108(O6) A1808, A1809, A1810, A1811 U:A1095 G:A1106, C:A1107
2qbh A1602 Ob G:A1417(O6) A1888, A1889, A1890, A1891, A1892 G:A1416, G:A1415 G:A1416, U:A1481, G:A1482
2qbi B2976 Ob U:B2028(O4) B3352, B3353, B3354, B3355 G:B2027
2qbi B2939 Ob C:B2499(O2) B3180, B3181, B3182, B3183, B3184 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qbi B2936 Ob U:B746(O4) B3166, B3167, B3168, B3169, D210 C:B2610, C:B2611, U:B744 G:B745
2qbj A1578 Ob G:A1370(O6) A1785, A1786, A1787, A1788, A1789 U:A1351, G:A1371, U:A1372
2qbj A1603 Ob G:A1417(O6) A1897, A1898, A1899, A1900, A1901 G:A1415 G:A1482, G:A1416
2qbk B2984 Ob C:B2499(O2) B3398, B3399, B3400, B3401, B3402 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qbk B2972 Ob U:B746(O4) B3345, B3346, B3347, B3348, B3349 C:B2610, C:B2611, U:B744 G:B745
2qex 08053 Ob G:0471(O6) 04251, 05469, 09027, 09066, 09873 A:0882 G:0469, C:0881 U:0470, U:0883
2qou A1601 Ob U:A1358(O4) A2180, A2181, A2182, A2183, A2184 A:A1357 C:A1359, A:A1357, G:A976
2qou A1575 Ob G:A1370(O6) A2058, A2059, A2060, A2061, A2062 U:A1351, G:A1371
2qou A1561 Ob G:A1050(O6) A1985, A1986, A1987, A1988, A1989 G:A1207, C:A1051, G:A1048
2qou A1602 Ob G:A1417(O6) A2185, A2186, A2187, A2188, A2189 G:A1416, G:A1415 G:A1416, G:A1482
2qov B2939 Ob C:B2499(O2) B3182, B3183, B3184, B3185, B3186 G:B2032 C:B2055, U:B2500, G:B2454, G:B2032
2qov B2936 Ob U:B746(O4) B3167, B3168, B3169, B3170, B3171 U:B744, C:B2610, C:B2611
2qow A1581 Ob G:A1417(O6) A2072, A2073, A2074, A2075, A2076 G:A1416, G:A1415 G:A1482, G:A1416
2qow A1594 Ob G:A1370(O6) A2138, A2139, A2140, A2141, A2142 U:A1372, U:A1351, G:A1371
2qox B2983 Ob C:B2499(O2) B3395, B3396, B3397, B3398, B3399 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454
2qoy A1602 Ob G:A1417(O6) A2187, A2188, A2189, A2190, A2191 G:A1416, G:A1415 G:A1482, G:A1416
2qoy A1561 Ob G:A1050(O6) A1987, A1988, A1989, A1990, A1991 U:A1049 G:A1048
2qoy A1575 Ob G:A1370(O6) A2060, A2061, A2062, A2063, A2064 U:A1348 U:A1351, A:A1350, G:A1371, U:A1372
2qoz B2939 Ob C:B2499(O2) B3674, B3675, B3676, B3677, B3678 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qoz B2936 Ob U:B746(O4) B3660, B3661, B3662, B3663, D3170 U:B744, C:B2610, C:B2611, U:B2580
2qp0 A1581 Ob G:A1417(O6) A2071, A2072, A2073, A2074, A2075 G:A1415, G:A1416 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>