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

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Representative site 2qbc:B3001, See in JSmolMgRNA representative site for type 6BO            Click on the image to toggle views


Site type: 6Bout

Schematic drawing for
6Bout

MgRNA type 6BO
List of all 78 Mg2+ binding sites with the site type 6Bout 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 3 of 4 | | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3ccv 08028 6Bout 03634, 03659, 03680, 03682, 07823, 09292 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
3cpw 08028 6Bout 04064, 04087, 04106, 04108, 08239, 09763 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
3cxc 08038 6Bout 03269, 04574, 04598, 04619, 04621, 08708 U:02115, U:02276, G:02271, G:02275, U:02116, A:02274
3i1n A2969 6Bout A3347, A3348, A3349, A3350, A3351, A3352 G:A2238, G:A2242, U:A2075, U:A2074, U:A2243, A:A2241
3i1r A2969 6Bout A3345, A3346, A3347, A3348, A3349, A3350 G:A2238, G:A2242, U:A2075, U:A2074, U:A2243, A:A2241
3i20 A2969 6Bout A3345, A3346, A3347, A3348, A3349, A3350 G:A2238, G:A2242, U:A2075, U:A2074, U:A2243, A:A2241
3ofr A2969 6Bout A3342, A3343, A3344, A3345, A3346, A3347 G:A2238, G:A2242, U:A2075, U:A2074, U:A2243, A:A2241
3ofz A2967 6Bout A3334, A3335, A3336, A3337, A3338, A3339 U:A2075, G:A2238, G:A2242, U:A2074, U:A2243, A:A2241
3orb A2968 6Bout A3342, A3343, A3344, A3345, A3346, A3347 G:A2238, G:A2242, U:A2075, U:A2074, U:A2243, A:A2241
3v23 A3600 6Bout A4994, A4995, A4996, A4997, A4998, A4999 A:A2241, U:A2074, U:A2243, G:A2238, G:A2242, U:A2075
3v23 A3459 6Bout A4485, A4486, A4487, A4488, A4489, A4490 U:A271, G:A271, G:A271, C:A271, G:A271, G:A271
3v25 A3268 6Bout A3621, A3622, A3623, A3624, A3625, A3626 G:A2238, G:A2242, A:A2241, U:A2074, U:A2243, U:A2075
3v27 A3414 6Bout A4278, A4279, A4280, A4281, A4282, A4283 A:A2241, U:A2074, U:A2243, G:A2242, U:A2075, G:A2238
3v2d A3308 6Bout A4548, A4549, A4550, A4551, A4552, A4553 A:A2241, U:A2074, U:A2243, G:A2238, G:A2242, U:A2075
3v2f A3185 6Bout A3869, A3870, A3871, A3872, A3873, A3874 G:A2238, G:A2242, A:A2241, U:A2074, U:A2243, U:A2075
4dha A3611 6Bout A4408, A4409, A4410, A4411, A4412, A4413 A:A2241, U:A2074, U:A2243, G:A2238, G:A2242, U:A2075
4dhc A3397 6Bout A3851, A3852, A3853, A3854, A3855, A3856 G:A2238, G:A2242, A:A2241, U:A2074, U:A2243, U:A2075
4gar A3064 6Bout A3502, A3503, A3504, A3505, A3506, A3507 G:A2242, G:A2238, A:A2241, U:A2074, U:A2075, U:A2243
4peb A3065 6Bout A3503, A3504, A3505, A3506, A3507, A3508 G:A2238, A:A2241, G:A2242, U:A2075, U:A2074, U:A2243
4qcn A3357 6Bout A4250, A4251, A4252, A4253, A4254 A:A2253, G:A2250, G:A2254, U:A2255, U:A2096, U:A2097
4qcp A3563 6Bout A4794, A4795, A4796, A4797, A4798, A4799 G:A2238, G:A2242, A:A2241, U:A2074, U:A2243, U:A2075
4qd1 A3571 6Bout A4645, A4646, A4647, A4648, A4649, A4650 G:A2238, G:A2242, A:A2241, U:A2074, U:A2243, U:A2075
4tom A3065 6Bout A3500, A3501, A3502, A3503, A3504, A3505 G:A2238, G:A2242, U:A2075, U:A2074, U:A2243, A:A2241
4tov A3067 6Bout A3500, A3501, A3502, A3503, A3504, A3505 G:A2238, A:A2241, G:A2242, U:A2074, U:A2075, U:A2243
4tox A3067 6Bout A3498, A3499, A3500, A3501, A3502, A3503 G:A2238, G:A2242, U:A2075, U:A2074, U:A2243, A:A2241

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>