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

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Representative site 2qan:A2288, See in JSmolMgRNA representative site for type 4BO            Click on the image to toggle views

Site type: 4Bout

Schematic drawing for

MgRNA type 4BO
List of all 105 Mg2+ binding sites with the site type 4Bout 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
1egk C13 4Bout C87, C88, C90, C91, C92, D89 U:C115, G:C116, DA:D126, DG:D124
1ehz A510 4Bout A712, A713, A714, A715, A716 G:A3, G:A4, U:A68, U:A69
1hr2 A20 4Bout A365, A366, A367, A368, A369, A370 U:A144, U:A156, U:A157, G:A158
1yls B243 4Bout A361, A366, B362, B363, B364, B365 G:A108, G:B202, G:B203, G:B201
2g91 B192 4Bout A139, A140, B138, B141 G:A2, U:A3, G:B15, C:B14
2g91 A191 4Bout A116, A120, A162, A180, A184, B122 G:A4, C:A5, U:A3, U:B12
2nug F513 4Bout E522, F542, F543, F544, F545, F552 G:E26, G:F26, U:E25, U:F25
2qan A2288 4Bout A2289, A2290, A2291, A2292, A2293, A2294 G:A1525, G:A1526, C:A1509, C:A1524
2qan A2084 4Bout A2085, A2086, A2087, A2088, A2089, A2090 G:A1207, G:A1050, C:A1051, G:A1048
2qao B3357 4Bout B3912, B3913, B3914, B3915, B3916, B3917 G:B17, U:B18, U:B521, A:B522
2qbb A2084 4Bout A2437, A2438, A2439, A2440, A2441, A2442 G:A1050, G:A1207, G:A1048, C:A1051
2qbc B3357 4Bout B3910, B3911, B3912, B3913, B3914, B3915 U:B18, U:B521, G:B17, A:B522
2qbc B3396 4Bout B3943, B3944, B3945, B3946, B3947, B3948 A:B739, U:B755, A:B756, G:B757
2qbd A2031 4Bout A2032, A2033, A2034, A2035, A2036, A2037 U:A593, U:A594, G:A645, G:A646
2qbe B3014 4Bout B3624, B3625, B3626, B3627, B3628, B3629 G:B1259, A:B1260, U:B580, U:B1258
2qbi B2984 4Bout B3390, B3391, B3392, B3393, B3394, B3395 G:B2549, G:B2550, G:B2557, C:B2558
2qov B2918 4Bout B3076, B3077, B3078, B3079, B3080, B3081 U:B521, A:B522, G:B17, U:B18
2qp0 A1590 4Bout A2113, A2114, A2115, A2116, A2117 G:A1048, G:A1050, G:A1207, C:A1208
2qp1 B2971 4Bout B3847, B3848, B3849, B3850, B3851, B3852 U:B755, A:B756, A:B739, G:B757
2z4l B2923 4Bout B3096, B3097, B3098, B3099, B3100, B3101 G:B2010, U:B2011, G:B2012, A:B2009
2z4n B2966 4Bout B3309, B3310, B3311, B3312, B3313, B3314 G:B17, U:B18, U:B521, A:B522
3df4 B3396 4Bout B4397, B4398, B4399, B4400, B4401, B4402 A:B756, G:B757, A:B739, U:B755
3i1p A2925 4Bout A3148, A3149, A3150, A3151, A3152, A3153 U:A755, G:A757, A:A739, A:A756
3i1r A2924 4Bout A3139, A3140, A3141, A3142, A3143, A3144 U:A755, A:A756, A:A739, G:A757
3i1t A2980 4Bout A3400, A3401, A3402, A3403, A3404, A3405 C:A2496, G:A2454, G:A2455, A:A2453

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>