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

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Representative site 3df2:B3464, See in JSmolMgRNA representative site for type 3BO            Click on the image to toggle views


Site type: 3Bout

Schematic drawing for
3Bout

MgRNA type 3BO
List of all 341 Mg2+ binding sites with the site type 3Bout 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 2 of 14 | | | 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
1vs6 B2947 3Bout B3216, B3217, B3218, B3219, B3220, B3221 G:B43, U:B434, A:B42
1vs6 B2918 3Bout B3077, B3078, B3079, B3080, B3081, B3082 U:B521, G:B17, U:B18
1vs6 B2984 3Bout B3394, B3395, B3396, B3397, B3398, B3399 G:B2550, G:B2557, C:B2558
1vs8 B2969 3Bout B3333, B3334, B3335, B3336, B3337, B3338 A:B756, A:B739, G:B757
1vs8 B2968 3Bout B3327, B3328, B3329, B3330, B3331, B3332 C:B650, G:B651, U:B652
1vs8 B2967 3Bout B3321, B3322, B3323, B3324, B3325, B3326 U:B580, U:B1258, G:B1259
1vs8 B2951 3Bout B3239, B3240, B3241, B3242, B3243, B3244 G:B2550, G:B2557, G:B2549
1vt2 A2925 3Bout A3146, A3147, A3148, A3149, A3150, A3151 G:A757, A:A739, A:A756
1vt2 B590 3Bout B591, B592, B593, B595, V594 U:B95, G:B96, U:B80
1yjn 08063 3Bout 04199, 07005, 07430, 07745, 07823, C8673 G:01364, U:01362, G:01363
1yls D343 3Bout C410, D405, D406, D407, D408, D409 G:C108, G:D202, G:D203
2aw4 B2947 3Bout B3212, B3213, B3214, B3215, B3216, B3217 G:B43, U:B434, A:B42
2aw4 B2924 3Bout B3107, B3108, B3109, B3110, B3111, B3112 A:B756, A:B739, G:B757
2aw4 B2918 3Bout B3074, B3075, B3076, B3077, B3078, B3079 U:B521, G:B17, U:B18
2awb B2964 3Bout B3303, B3304, B3305, B3306, B3307, B3308 C:B16, G:B17, U:B18
2awb B2952 3Bout B3243, B3244, B3245, B3246, B3247, B3248 G:B2550, G:B2557, G:B2549
2awb B2970 3Bout B3334, B3335, B3336, B3337, B3338, B3339 A:B756, A:B739, G:B757
2b8s A103 3Bout A229, A254, A269, B215, B262, B315 U:A11, G:A12, U:B11
2i2p A1600 3Bout A1885, A1886, A1887, A1888, A1889 U:A1358, A:A1357, A:A1363
2i2t B2924 3Bout B3117, B3118, B3119, B3120, B3121, B3122 A:B739, A:B756, G:B757
2i2t B2984 3Bout B3400, B3401, B3402, B3403, B3404, B3405 G:B2550, G:B2557, G:B2549
2i2u A1597 3Bout A1860, A1861, A1862, A1863, A1864 G:A1356, A:A1357, G:A1355
2i2v B2956 3Bout B3270, B3271, B3272, B3273, B3274, B3275 A:B42, G:B43, U:B434
2i2v B2964 3Bout B3310, B3311, B3312, B3313, B3314, B3315 G:B17, U:B521, A:B522
2i2v B2968 3Bout B3331, B3332, B3333, B3334, B3335, B3336 A:B1260, U:B580, U:B1258

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>