`

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

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 3df4:B3320, See in JSmolMgRNA representative site for type 3PO-RO-4BO     Click on the image to toggle views


Site type: 3Pout·Rout·4Bout

Schematic drawing for
3Pout·Rout·4Bout

MgRNA type 3PO-RO-4BO
List of all 16 Mg2+ binding sites with the site type 3Pout·Rout·4Bout 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 1
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1vt2 A2920 3Pout·Rout·4Bout A3121, A3122, A3123, A3124, A3125, A3126 A:A582, A:A1253, G:A583 C:A1251 G:A583, C:A584, G:A585, A:A582
2qba B3302 3Pout·Rout·4Bout B3859, B3860, B3861, B3862, B3863, B3864 A:B1253, A:B582, G:B583 C:B1251 C:B584, G:B585, A:B582, G:B583
2qbi B2956 3Pout·Rout·4Bout B3258, B3259, B3260, B3261, B3262, B3263 A:B1253, A:B582, G:B583 C:B1251 G:B583, C:B584, G:B585, A:B582
3df4 B3320 3Pout·Rout·4Bout B4321, B4322, B4323, B4324, B4325, B4326 A:B582, G:B583, A:B1253 C:B1251 C:B584, G:B585, A:B582, G:B583
3i1p A2920 3Pout·Rout·4Bout A3124, A3125, A3126, A3127, A3128, A3129 A:A582, A:A1253, G:A583 C:A1251 G:A583, C:A584, G:A585, A:A582
3i22 A2920 3Pout·Rout·4Bout A3121, A3122, A3123, A3124, A3125, A3126 A:A582, A:A1253, G:A583 C:A1251 C:A584, G:A585, A:A582, G:A583
3oas A2920 3Pout·Rout·4Bout A3121, A3122, A3123, A3124, A3125, A3126 A:A582, A:A1253, G:A583 C:A1251 G:A583, C:A584, G:A585, A:A582
3ofd A2920 3Pout·Rout·4Bout A3121, A3122, A3123, A3124, A3125, A3126 A:A582, A:A1253, G:A583 C:A1251 C:A584, G:A585, A:A582, G:A583
3og0 A2919 3Pout·Rout·4Bout A3118, A3119, A3120, A3121, A3122, A3123 A:A582, A:A1253, G:A583 C:A1251 G:A583, C:A584, G:A585, A:A582
4peb A3002 3Pout·Rout·4Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A28, A:A447 A:A447 G:A473, G:A474, U:A29, G:A30
4qcn A3727 3Pout·Rout·4Bout A5236, A5237, A5238, A5239, A5240, A5241 A:A473, A:A28, U:A29 A:A473 G:A499, U:A29, G:A500, G:A30
4qcr A3754 3Pout·Rout·4Bout A5268, A5269, A5270, A5271, A5272, A5273 A:A473, A:A28, U:A29 A:A473 G:A499, U:A29, G:A500, G:A30
4tov A3003 3Pout·Rout·4Bout A3207, A3208, A3209, A3210, A3211, A3212 A:A28, U:A29, A:A447 A:A447 G:A473, G:A474, U:A29, G:A30
4tp1 A3003 3Pout·Rout·4Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A28, A:A447 A:A447 G:A473, G:A474, U:A29, G:A30
4tp7 A3003 3Pout·Rout·4Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A28, A:A447 A:A447 U:A29, G:A473, G:A30, C:A31
4tp9 A3003 3Pout·Rout·4Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A28, A:A447 A:A447 G:A473, G:A474, U:A29, G:A30

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>