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

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Representative site 2qbb:A2049, See in JSmolMgRNA representative site for type 2PO-BO         Click on the image to toggle views


Site type: 2Pout·Bout

Schematic drawing for
2Pout·Bout

MgRNA type 2PO-BO
List of all 169 Mg2+ binding sites with the site type 2Pout·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"
Page 3 of 7 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3ofb A1 2Pout·Bout A2, A3, A4, A1576, A1577, T87 G:A258, G:A259 G:A260
3ofd A2952 2Pout·Bout A3263, A3264, A3265, A3266, A3267 G:A1456, A:A1453 G:A1456
3ofo A1561 2Pout·Bout A1711, A1712, A1713, A1714, A1715 A:A1433, A:A1434 G:A1435
3ofp A1557 2Pout·Bout A1684, A1685, A1686, A1687, A1688, E162 U:A20, G:A21 G:A21
3ofq A3029 2Pout·Bout A3600, A3601, A3602, A3603 U:A1188, A:A1189 G:A1190
3ofq A3002 2Pout·Bout A3498, A3499, A3500, A3501, A3502, A3503 C:A2047, C:A2616 G:A2048
3ofx A1562 2Pout·Bout A1714, A1715, A1716, A1717, A1718 A:A1433, A:A1434 G:A1435
3ofy A1557 2Pout·Bout A1687, A1688, A1689, A1690, A1691, E159 U:A20, G:A21 G:A21
3og0 A2951 2Pout·Bout A3263, A3264, A3265, A3266, A3267 G:A1456, A:A1453 G:A1456
3og0 A3000 2Pout·Bout A3499, A3500, A3501, A3502, A3503, A3504 C:A2616, C:A2047 G:A2048
3or9 A1563 2Pout·Bout A1715, A1716, A1717, A1718, A1719 A:A1433, A:A1434 G:A1435
3oxm A109 2Pout·Bout A119, A120, A121, A122, A123, A143 A:A64, A:A37 A:A37
3r8s A3019 2Pout·Bout A3624, A3625, A3626, A3627, A3628, 2677 U:A686, C:A687 G:A770
3td0 B4000 2Pout·Bout A4002, A4006, B4001, B4003, B4004, B4005 C:B32, G:B33 G:B33
3td0 A2000 2Pout·Bout A2001, A2002, A2003, A2004, A2005, B2006 G:A13, C:A12 G:A13
3v23 A3361 2Pout·Bout A4114, A4115, A4116, A4117, A4118 A:A340, G:A341 G:A341
3v23 A3455 2Pout·Bout A4472, A4473, A4474, A4475, A4476, A4477 C:A2774, A:A2775 A:A2775
3v23 A3610 2Pout·Bout A5053, A5054, A5055, A5056, A5057, A5058 G:A1904, G:A2597 G:A2595
3v23 A3346 2Pout·Bout A4058, A4059, A4060, A4061, A4062, A4063 G:A1283, U:A1282 G:A1283
3v25 A3321 2Pout·Bout A3826, A3827, A3828, A3829 G:A1904, G:A2597 G:A2595
3v27 A3385 2Pout·Bout A4161, A4162, A4163, A4164, A4165, A4166 C:A1318, C:A1330 G:A1319
3v27 A3642 2Pout·Bout A5293, A5294, A5295, A5296, A5297 G:A1488, G:A1487 U:A1489
3v27 A3361 2Pout·Bout A4075, A4076, A4077, A4078, A4079 G:A2482, C:A2483 G:A2484
3v27 A3499 2Pout·Bout A4634, A4635, A4636, A4637, A4638, A4639 G:A2597, G:A1904 G:A2595
3v27 A3529 2Pout·Bout A4774, A4775, A4776, A4777, A4778, A4779 A:A1579, A:A1580 G:A1416

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>