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

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Representative site 3df2:B3007, See in JSmolMgRNA representative site for type 7BO            Click on the image to toggle views

Site type: 7Bout

Schematic drawing for

MgRNA type 7BO
List of all 7 Mg2+ binding sites with the site type 7Bout 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
2i2v B2905 7Bout B3024, B3025, B3026, B3027, B3028, B3029 U:B2075, A:B2077, G:B2238, G:B2242, U:B2243, A:B2241, U:B2074
2qp1 B2905 7Bout B3522, B3523, B3524, B3525, B3526, B3527 U:B2075, A:B2077, G:B2238, G:B2242, U:B2243, A:B2241, U:B2074
3df2 B3007 7Bout B4008, B4009, B4010, B4011, B4012, B4013 U:B2074, G:B2238, A:B2241, G:B2242, U:B2075, A:B2077, U:B2243
4gau A3063 7Bout A3500, A3501, A3502, A3503, A3504, A3505 G:A2238, A:A2241, G:A2242, U:A2243, U:A2075, U:A2074, A:A2077
4qct A3582 7Bout A4821, A4822, A4823, A4824, A4825, A4826 A:A2077, G:A2238, G:A2242, A:A2241, U:A2074, U:A2243, U:A2075
4tox A3073 7Bout A3528, A3529, A3530, A3531, A3532 C:A2055, U:A2500, U:A2504, G:A2032, G:A2454, C:A2499, A:A2453
4tp7 A3067 7Bout A3495, A3496, A3497, A3498, A3499, A3500 A:A2077, G:A2238, G:A2242, U:A2074, U:A2075, U:A2243, A:A2241

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>