`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 3df3:A2016, See in JSmolMgRNA representative site for type 2PO-3BO Click on the image to toggle views


Site type: 2Pout·3Bout

Schematic drawing for
2Pout·3Bout
MgRNA type 2PO-3BO
List of all 199 Mg2+ binding sites with the site type 2Pout·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 5 of 8 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3ofr A2921 2Pout·3Bout A3123, A3124, A3125, A3126, A3127, E202 A:A616, A:A608 G:A617, G:A618, G:A619
3ofx A1544 2Pout·3Bout A1626, A1627, A1628, A1629, A1630, A1631 G:A803, U:A804 G:A771, U:A772, G:A773
3ofy A1537 2Pout·3Bout A1589, A1590, A1591, A1592, A1593, A1594 A:A415, G:A416 G:A417, G:A416, U:A426
3ofy A1549 2Pout·3Bout A1648, A1649, A1650, A1651, N101, N102 A:A1360, C:A1359 C:A980, G:A1361, A:A1360
3ofy A1544 2Pout·3Bout A1623, A1624, A1625, A1626, A1627, A1628 G:A803, U:A804 G:A771, U:A772, G:A773
3ofz A2920 2Pout·3Bout A3119, A3120, A3121, A3122, A3123, A3124 A:A616, A:A608 G:A617, G:A618, G:A619
3ora A1537 2Pout·3Bout A1593, A1594, A1595, A1596, A1597, A1598 A:A415, G:A416 G:A417, G:A425, G:A416
3ora A1544 2Pout·3Bout A1627, A1628, A1629, A1630, A1631, A1632 G:A803, U:A804 G:A771, U:A772, G:A773
3ora A1535 2Pout·3Bout A1582, A1583, A1584, A1585, A1586, A1587 A:A315, A:A329 G:A319, A:A320, G:A318
3orb A2921 2Pout·3Bout A3124, A3125, A3126, A3127, A3128, A3129 A:A616, A:A608 G:A617, G:A618, G:A619
3q3z A83 2Pout·3Bout A103, A105, A106, A113, A115, A116 G:A73, C:A72 G:A12, A:A74, G:A73
3r8s A2996 2Pout·3Bout A3528, A3529, A3530, A3531, A3532, A3533 A:A1572, G:A1422 G:A1423, G:A1424, G:A1425
3r8s A2921 2Pout·3Bout A3186, A3187, A3188, A3189, A3190, A3191 G:A617, A:A616 G:A617, G:A618, G:A619
3r8t A2995 2Pout·3Bout A3499, A3500, A3501, A3502, A3503, A3504 A:A1572, G:A1422 G:A1423, G:A1425, G:A1424
3r8t A3036 2Pout·3Bout A3668, A3669, A3670, A3671, A3672, A3673 A:A2740, A:A2741 G:A2763, G:A2742, U:A2743
3v25 A3425 2Pout·3Bout A4179, A4180, A4181, A4182 C:A2452, A:A2453 A:A2453, G:A2454, A:A2497
3v27 A3321 2Pout·3Bout A3904, A3905, A3906, A3907, A3908, A3909 A:A299, C:A336 G:A338, A:A299, A:A300
3v27 A3409 2Pout·3Bout A4260, A4261, A4262, A4263, A4264 U:A1397, C:A1398 C:A1386, G:A1401, G:A1400
3v27 A3423 2Pout·3Bout A4315, A4316, A4317, A4318, A4319, A4320 A:A1634, G:A1627 G:A1628, U:A1629, G:A1630
3v29 A3433 2Pout·3Bout A4151, A4152, A4153, A4154, A4155, A4156 A:A2360, C:A2359 A:A2361, U:A2357, A:A2360
3v29 A3425 2Pout·3Bout A4121, A4122, A4123, A4124, A4125 A:A1572, G:A1421 G:A1423, G:A1424, G:A1425
3v29 A3574 2Pout·3Bout A4673, A4674, A4675, A4676, A4677, A4678 C:A1398, U:A1397 G:A1401, G:A1400, G:A1385
3v2c A1680 2Pout·3Bout A2036, A2037, A2038, A2039 U:A582, A:A583 G:A585, G:A584, U:A757
3v2d A3499 2Pout·3Bout A5123, A5124, A5125, A5126, A5127 A:A2005, G:A2004 G:A1650, G:A1651, G:A1649
3v2d A3554 2Pout·3Bout A5274, A5275, A5276, A5277, A5278, A5279 A:A2360, C:A2359 U:A2357, A:A2361, C:A2356

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>