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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 1 of 4 | « Previous | | 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
2i2p A1548 6Bout A1628, A1629, A1630, A1631, A1632, A1633 G:A645, G:A646, G:A592, U:A644, U:A593, U:A594
4tp4 A1610 6Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A646, U:A593, U:A594, G:A645, G:A592, U:A644
2qan A2114 6Bout A2115, A2116, A2117, A2118, A2119, A2120 U:A594, G:A645, G:A592, U:A593, G:A646, C:A647
2qox B2905 6Bout B3015, B3016, B3017, B3018, B3019, B3020 U:B2075, G:B2238, G:B2242, U:B2243, A:B2241, U:B2074
2awb B2905 6Bout B3015, B3016, B3017, B3018, B3019, B3020 G:B2238, G:B2242, U:B2243, A:B2241, U:B2074, U:B2075
2qbk B2905 6Bout B3017, B3018, B3019, B3020, B3021, B3022 G:B2238, G:B2242, A:B2241, U:B2074, U:B2075, U:B2243
1vs8 B2905 6Bout B3014, B3015, B3016, B3017, B3018, B3019 G:B2238, G:B2242, U:B2243, A:B2241, U:B2074, U:B2075
2i2t B2906 6Bout B3028, B3029, B3030, B3031, B3032, B3033 G:B2238, A:B2241, G:B2242, U:B2075, A:B2077, U:B2243
2qbi B2906 6Bout B3021, B3022, B3023, B3024, B3025, B3026 U:B2074, U:B2243, A:B2241, G:B2242, U:B2075, G:B2238
2z4n B2906 6Bout B3017, B3018, B3019, B3020, B3021, B3022 U:B2075, G:B2238, G:B2242, U:B2243, A:B2241, U:B2074
2qov B2906 6Bout B3020, B3021, B3022, B3023, B3024, B3025 U:B2074, U:B2243, A:B2241, U:B2075, G:B2238, G:B2242
2z4l B2907 6Bout B3021, B3022, B3023, B3024, B3025, B3026 U:B2074, U:B2243, A:B2241, G:B2242, U:B2075, G:B2238
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
3i1n A2969 6Bout A3347, A3348, A3349, A3350, A3351, A3352 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
3i1r A2969 6Bout A3345, A3346, A3347, A3348, A3349, A3350 G:A2238, G:A2242, U:A2075, U:A2074, U:A2243, A:A2241
2qbc B3001 6Bout B3620, B3621, B3622, B3623, B3624, B3625 G:B2238, G:B2242, A:B2241, U:B2074, U:B2075, U:B2243
2qba B3007 6Bout B3619, B3620, B3621, B3622, B3623, B3624 U:B2074, U:B2243, A:B2241, G:B2242, U:B2075, G:B2238
2qbe B3007 6Bout B3618, B3619, B3620, B3621, B3622, B3623 U:B2243, A:B2241, U:B2074, U:B2075, G:B2238, G:B2242
2qam B3007 6Bout B3618, B3619, B3620, B3621, B3622, B3623 U:B2074, U:B2243, A:B2241, G:B2242, U:B2075, G:B2238
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
4tom A3065 6Bout A3500, A3501, A3502, A3503, A3504, A3505 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>