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

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Representative site 2z4n:B2988, See in JSmolMgRNA representative site for type 5PO-BO         Click on the image to toggle views

Site type: 5Pout·Bout

Schematic drawing for

MgRNA type 5PO-BO
List of all 6 Mg2+ binding sites with the site type 5Pout·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
2aw4 B2935 5Pout·Bout B3160, B3161, B3162, B3163, B3164, B3165 U:B2613, C:B2050, A:B2051, G:B2578, A:B2614 A:B2614
2z4n B2988 5Pout·Bout B3411, B3412, B3413, B3414, B3415, B3416 U:B2613, C:B2050, A:B2051, G:B2578, A:B2614 A:B2051
3r8t A2964 5Pout·Bout A3354, A3355, A3356, A3357, A3358, A3359 C:A2050, A:A2614, A:A2051, G:A2578, U:A2613 A:A2051
4dr5 A1628 5Pout·Bout A1973, A1974, A1975, A1976 A:A563, G:A557, U:A560, C:A562, G:A558 G:A566
4gar A3049 5Pout·Bout A3431, A3432, A3433, A3434, A3435, A3436 G:A2550, C:A2551, A:A1987, C:A1986, A:A1669 G:A1954
4tpf A3121 5Pout·Bout A3738, A3739, A3740, A3741 C:A192, A:A199, U:A2243, U:A193, C:A198 A:A195

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>