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

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Representative site 3df2:B3464, See in JSmolMgRNA representative site for type 3BO            Click on the image to toggle views


Site type: 3Bout

Schematic drawing for
3Bout

MgRNA type 3BO
List of all 341 Mg2+ binding sites with the site type 3Bout 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 14 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3cgs B1 3Bout A13, A14, B26, B27, B28, B29 G:B20, G:A5, U:B19
3ssf A14 3Bout A44, A45, A46, A57 A:A10, G:A11, G:A12
1hr2 B21 3Bout B374, B375, B376, B377, B378, B379 G:B158, U:B157, U:B144
1dnt A21 3Bout A146, A147, A148, A149, A150, B151 DT:A4, DG:A3, DT:B16
1dno B22 3Bout A205, B203, B204, B206, B207, B208 DT:A6, G:B13, DT:B14
1hr2 B23 3Bout B380, B381, B382, B383, B384, B385 U:B243, G:B242, A:B230
1dno A24 3Bout A215, A216, A217, A218, B219, B220 DT:A4, G:A3, DT:B16
1hr2 A24 3Bout A377, A378, A379, A380, A381, A382 G:A134, U:A135, U:A182
1hr2 A26 3Bout A383, A384, A385, A386, A387, A388 G:A111, G:A112, G:A110
3hhn C60 3Bout C59, C61, C62, C63, C64, C65 G:C81, A:C80, G:C75
4a1a 066 3Bout 05507, 05508, 05509, 05510, 05511, 05512 G:216, U:217, G:215
4a1c 066 3Bout 05331, 05332, 05333, 05334, 05335, 05336 G:215, G:216, U:217
4a17 066 3Bout 05635, 05636, 05637, 05638, 05639, 05640 G:215, G:216, U:217
4a1e 066 3Bout 05571, 05572, 05573, 05574, 05575, 05576 G:216, G:215, U:217
2b8s A103 3Bout A229, A254, A269, B215, B262, B315 U:A11, G:A12, U:B11
3ox0 A110 3Bout A146, A147, A148, A149, A150, A151 G:A25, G:A26, U:A27
3oxm A112 3Bout A124, A125, A129, A144, A145, A146 U:A46, G:A47, G:A55
4a1c 0117 3Bout 05619, 05620, 05621, 05622, 05623, 05624 G:382, G:383, A:381
4a1a 0117 3Bout 05859, 05860, 05861, 05862, 05863, 05864 G:382, G:383, A:381
3i1t B119 3Bout B627, B628, B629, B630, B631 U:B80, U:B95, G:B96
3hhn C123 3Bout C122, C124, C125, C126, C127, C128 G:C2, G:C1, A:C-1
3ivk M124 3Bout M150, M151, M152, M153, M154, M155 G:M72, A:M73, G:M105
3ivk C124 3Bout C150, C151, C152, C153, C154, C155 G:C72, A:C73, G:C105
3ivk M125 3Bout M156, M157, M158, M159, M160, M161 A:M80, G:M81, G:M75
3ivk C125 3Bout C156, C157, C158, C159, C160, C161 A:C80, G:C81, G:C75

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>