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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qbg:B2930, See in JSmolMgRNA representative site for type PO-4BO Click on the image to toggle views


Site type: Pout·4Bout

Schematic drawing for
Pout·4Bout
MgRNA type PO-4BO
List of all 135 Mg2+ binding sites with the site type Pout·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"
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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
3ofp A1537 Pout·4Bout A1589, A1590, A1591, A1592, A1593, A1594 A:A415 G:A417, G:A425, G:A416, U:A426
3ofr A2986 Pout·4Bout A3419, A3420, A3421, A3422, A3423, A3424 A:A933 G:A843, G:A841, U:A842, A:A936
3ofy A1543 Pout·4Bout A1617, A1618, A1619, A1620, A1621, A1622 G:A645 G:A646, G:A645, G:A592, U:A593
3og0 A2924 Pout·4Bout A3143, A3144, A3145, A3146, A3147, A3148 U:A755 U:A755, G:A757, A:A739, A:A756
3og0 A2978 Pout·4Bout A3396, A3397, A3398, A3399, A3400, A3401 G:A2454 G:A2454, G:A2455, C:A2496, A:A2453
3og0 A2941 Pout·4Bout A3222, A3223, A3224, A3225, A3226, A3227 U:A1267 A:A2009, G:A2010, U:A2011, G:A2012
3ora A1561 Pout·4Bout A1712, A1713, A1714, A1715, A1716 A:A1349 U:A1351, G:A1371, U:A1372, G:A1370
3r8t A3034 Pout·4Bout A3659, A3660, A3661, A3662, A3663, A3664 C:A1790 G:A1792, U:A1827, G:A1826, C:A1793
3v23 A3602 Pout·4Bout A5006, A5007, A5008, A5009, A5010, A5011 A:A103 G:A80, G:A81, G:A79, G:A82
3v26 A1711 Pout·4Bout A1947, A1948, A1949, A1950, A1951, A1952 C:A398 C:A36, U:A37, G:A35, G:A548
3v27 A3415 Pout·4Bout A4284, A4285, A4286, A4287, A4288 G:A186 G:A186, G:A187, G:A189, G:A188
3v29 A3572 Pout·4Bout A4661, A4662, A4663, A4664, A4665, A4666 U:A1267 G:A2010, G:A2009, U:A2011, G:A2012
3v2d A3659 Pout·4Bout A5537, A5538, A5539, A5540, A5541 A:A1701 G:A1703, G:A1702, G:A1699, G:A1763
3v2d A3684 Pout·4Bout A5625, A5626, A5627, A5628, A5629 G:A686 G:A690, G:A771, U:A688, A:A689
4a1a 0204 Pout·4Bout 06675, 06676, 06677, 06678, 06679, 06680 A:374 U:376, A:3101, G:3102, A:3100
4a1c 0204 Pout·4Bout 06291, 06292, 06293, 06294, 06295, 06296 A:374 U:376, A:3101, G:3102, A:3100
4bpe A5009 Pout·4Bout A2106, A2107, A2119, A2120, A2122, A2253 C:A577 G:A550, G:A580, C:A578, A:A579
4bpn A5009 Pout·4Bout A6189, A6197, A6200, A6207, A6214, A6221 C:A577 A:A579, G:A580, G:A550, C:A552
4dh9 A1870 Pout·4Bout A2091, A2092, A2093, A2094 A:A583 G:A584, G:A585, C:A756, U:A757
4dha A3710 Pout·4Bout A4766, A4767, A4768, A4769, A4770, A4771 A:A2360 U:A2357, A:A2361, C:A2356, G:A2362
4dha A3604 Pout·4Bout A4380, A4381, A4382, A4383, A4384 G:A686 G:A771, U:A688, A:A689, G:A690
4dhc A3581 Pout·4Bout A4392, A4393, A4394, A4395, A4396 G:A495 A:A482, G:A496, G:A494, G:A495
4dr2 A1751 Pout·4Bout A2388, A2389, A2390, A2391 A:A1360 C:A980, C:A979, A:A1360, G:A1361
4dr2 A1665 Pout·4Bout A2135, A2136, A2137, A2138, A2139 A:A583 G:A584, G:A585, C:A756, U:A757
4dr4 A1942 Pout·4Bout A2404, A2405, A2406, A2407, A2408, A2409 A:A642 G:A595, G:A594, G:A593, G:A592

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>