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

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Representative site 4ji8:A1909, See in JSmolMgRNA representative site for type 3PO-2RO-BO     Click on the image to toggle views

Site type: 3Pout·2Rout·Bout

Schematic drawing for

MgRNA type 3PO-2RO-BO
List of all 6 Mg2+ binding sites with the site type 3Pout·2Rout·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
1vt2 A2979 3Pout·2Rout·Bout A3396, A3397, A3398, A3399, A3400 G:A2447, C:A2501, G:A2502 A:A575, U:A576 G:A2502
3i1p A2979 3Pout·2Rout·Bout A3392, A3393, A3394, A3395, A3396 G:A2447, C:A2501, G:A2502 A:A575, U:A576 G:A2502
3oas A2978 3Pout·2Rout·Bout A3393, A3394, A3395, A3396, A3397 G:A2447, C:A2501, G:A2502 A:A575, U:A576 G:A2502
3og0 A2977 3Pout·2Rout·Bout A3391, A3392, A3393, A3394, A3395 G:A2447, C:A2501, G:A2502 A:A575, U:A576 G:A2502
4dhc A3486 3Pout·2Rout·Bout A4137, A4138, A4139, A4140 C:A1617, G:A1619, A:A1609 C:A1617, A:A1608 G:A1619
4ji8 A1909 3Pout·2Rout·Bout A2965, A2966, A2967, A2968, A2969, A2970 C:A536, C:A504, G:A505 A:A535, C:A522 G:A505

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>