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

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Representative site 3df2:B3382, See in JSmolMgRNA representative site for type 4PO-BO         Click on the image to toggle views

Site type: 4Pout·Bout

Schematic drawing for

MgRNA type 4PO-BO
List of all 125 Mg2+ binding sites with the site type 4Pout·Bout 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
1vs8 B2909 4Pout·Bout B3035, B3036, B3037, B3038, B3039, B3040 A:B1937, G:B1959, A:B1936, C:B1958 G:B1959
1vs8 B2910 4Pout·Bout B3041, B3042, B3043, B3044, B3045, B3046 C:B1986, A:B1669, A:B1987, C:B2551 G:B1954
1vt2 A2956 4Pout·Bout A3281, A3282, A3283, A3284, A3285, A3286 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954
2aw4 B2970 4Pout·Bout B3322, B3323, B3324, B3325, B3326, B3327 A:B1669, C:B1986, A:B1987, C:B2551 G:B1954
2awb B2909 4Pout·Bout B3036, B3037, B3038, B3039, B3040, B3041 A:B1937, G:B1959, A:B1936, C:B1958 G:B1959
2i2p A1559 4Pout·Bout A1681, A1682, A1683, A1684, A1685, A1686 U:A13, A:A16, U:A14, G:A15 U:A14
2i2t B2968 4Pout·Bout B3321, B3322, B3323, B3324, B3325, B3326 C:B1351, U:B1352, G:B1377, C:B1376 G:B1377
2i2t B2970 4Pout·Bout B3332, B3333, B3334, B3335, B3336, B3337 A:B1669, C:B1986, C:B2551, A:B1987 G:B1954
2i2t B2931 4Pout·Bout B3150, B3151, B3152, B3153, B3154, B3155 A:B1937, C:B1958, G:B1959, A:B1936 G:B1959
2i2u A1556 4Pout·Bout A1662, A1663, A1664, A1665, A1666, A1667 A:A768, U:A804, C:A805, A:A767 G:A769
2i2v B2910 4Pout·Bout B3051, B3052, B3053, B3054, B3055, B3056 C:B1986, A:B1669, A:B1987, C:B2551 G:B1954
2i2v B2920 4Pout·Bout B3100, B3101, B3102, B3103, B3104, B3105 C:B1351, U:B1352, G:B1377, C:B1376 G:B1377
2qam B3181 4Pout·Bout B3758, B3759, B3760, B3761, B3762, B3763 C:B2050, A:B2051, G:B2578, A:B2614 A:B2614
2qao B3033 4Pout·Bout B3645, B3646, B3647, B3648, B3649, B3650 C:B2551, A:B1987, A:B1669, C:B1986 G:B1954
2qba B3382 4Pout·Bout B3920, B3921, B3922, B3923, B3924, B3925 C:B1986, A:B1669, C:B2551, A:B1987 G:B1954
2qbc B3033 4Pout·Bout B3646, B3647, B3648, B3649, B3650, B3651 A:B1669, C:B1986, C:B2551, A:B1987 G:B1954
2qbc B3344 4Pout·Bout B3899, B3900, B3901, B3902, B3903, B3904 A:B1916, A:B1912, A:B1913, U:B1915 A:B1918
2qbc B3485 4Pout·Bout B4014, B4015, B4016, B4017, B4018, B4019 C:B2050, A:B2614, A:B2051, G:B2578 A:B2614
2qbg B2910 4Pout·Bout B3043, B3044, B3045, B3046, B3047, B3048 A:B1669, C:B1986, C:B2551, A:B1987 G:B1954
2qbi B2970 4Pout·Bout B3322, B3323, B3324, B3325, B3326, B3327 A:B1669, C:B1986, A:B1987, C:B2551 G:B1954
2qbi B2935 4Pout·Bout B3160, B3161, B3162, B3163, B3164, B3165 C:B2050, G:B2578, A:B2051, A:B2614 A:B2051
2qbi B2968 4Pout·Bout B3311, B3312, B3313, B3314, B3315, B3316 C:B1376, C:B1351, U:B1352, G:B1377 G:B1377
2qbk B2963 4Pout·Bout B3295, B3296, B3297, B3298, B3299, B3300 U:B1915, A:B1916, A:B1912, A:B1913 A:B1918
2qov B2935 4Pout·Bout B3161, B3162, B3163, B3164, B3165, B3166 G:B2578, C:B2050, A:B2051, U:B2613 A:B2614
2qp1 B2963 4Pout·Bout B3803, B3804, B3805, B3806, B3807, B3808 U:B1915, A:B1916, A:B1912, A:B1913 U:B1917

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>