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

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Representative site 3df4:B3602, See in JSmolMgRNA representative site for type PO-RO-2BO      Click on the image to toggle views

Site type: Pout·Rout·2Bout

Schematic drawing for

MgRNA type PO-RO-2BO
List of all 40 Mg2+ binding sites with the site type Pout·Rout·2Bout 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
1j1u B1503 Pout·Rout·2Bout B18, B77, B278, B359, B360, B361 A:B559 A:B559 G:B554, U:B555
1jj2 08076 Pout·Rout·2Bout 06397, 07389, 07390, 07445, 07446, 17875 U:01419 U:01418 G:01443, G:01444
1kc8 A8076 Pout·Rout·2Bout A6849, A7841, A7842, A7895, A7896, 37875 U:A1419 U:A1418 G:A1443, G:A1444
1kqs 08076 Pout·Rout·2Bout 06351, 07324, 07325, 07377, 07378, 17875 U:01419 U:01418 G:01443, G:01444
1m1k A8076 Pout·Rout·2Bout A6449, A7430, A7431, A7482, A7483, 37875 U:A1419 U:A1418 G:A1443, G:A1444
1m90 A8076 Pout·Rout·2Bout A6391, A7372, A7373, A7427, A7428, 37875 U:A1419 U:A1418 G:A1443, G:A1444
1n8r A8076 Pout·Rout·2Bout A7233, A8396, A8397, A8449, A8450, 37875 U:A1419 U:A1418 G:A1443, G:A1444
1nji A8076 Pout·Rout·2Bout A6848, A7834, A7835, A7891, A7892, 37875 U:A1419 U:A1418 G:A1443, G:A1444
1q82 A8076 Pout·Rout·2Bout A6336, A7314, A7366, A7367, 37875 U:A1419 U:A1418 G:A1444, G:A1443
1vq6 08076 Pout·Rout·2Bout 07065, 08123, 08124, 08173, 08174, 08175 U:01419 U:01418 G:01443, G:01444
1vq7 08076 Pout·Rout·2Bout 07100, 08154, 08155, 08207, 08208, 27875 U:01419 U:01418 G:01443, G:01444
2hw8 B202 Pout·Rout·2Bout B210, B217, B232, B237, B257, B282 A:B8 A:B26 A:B9, A:B8
2qal A2109 Pout·Rout·2Bout A2110, A2111, A2112, A2113, A2114 A:A1201 C:A1200 G:A1050, G:A1207
2z4m A1566 Pout·Rout·2Bout A1709, A1710, A1711, A1712, A1713, A1714 G:A1047 A:A1046 G:A1047, G:A1048
3cxc 08076 Pout·Rout·2Bout 07749, 08734, 08735, 08787, 08788, 17875 U:01419 U:01418 G:01443, G:01444
3df4 B3602 Pout·Rout·2Bout B4603, B4604, B4605, B4606, B4607, B4608 A:B973 A:B972 A:B820, A:B821
3ofb A1575 Pout·Rout·2Bout A1767, A1768, A1769, A1770, A1771 G:A354 C:A352 C:A330, G:A354
3ofq A3015 Pout·Rout·2Bout A3543, A3544, A3545, A3546, A3547, 2647 U:A686 A:A685 G:A770, G:A771
3ofr A2998 Pout·Rout·2Bout A3479, A3480, A3481, A3482, A3483, A3484 C:A1617 A:A1608 G:A1613, G:A1619
3ofy A1551 Pout·Rout·2Bout A1657, A1658, A1659, A1660 C:A1054 G:A1053 U:A1199, G:A1198
3ora A1575 Pout·Rout·2Bout A1773, A1774, A1775, A1776, A1777 G:A354 C:A352 C:A330, G:A354
3v23 A3589 Pout·Rout·2Bout A4928, A4929, A4930, A4931, A4932, A4933 A:A1142 U:A1142 G:A1017, G:A1016
3v27 A3518 Pout·Rout·2Bout A4718, A4719, A4720, A4721, A4722, A4723 A:A1528 G:A1527 U:A1540, G:A1541
3v27 A3608 Pout·Rout·2Bout A5108, A5109, A5110, A5111, A5112, A5113 A:A1142 U:A1142 G:A1016, G:A1017
3v27 A3561 Pout·Rout·2Bout A4921, A4922, A4923, A4924, A4925, A4926 U:A504 A:A503 G:A498, A:A482

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>