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

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Representative site 2qou:A1579, See in JSmolMgRNA representative site for type PO-RO-BO       Click on the image to toggle views

Site type: Pout·Rout·Bout

Schematic drawing for

List of all 28 Mg2+ binding sites with the site type Pout·Rout·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"
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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
2ao5 A198 Pout·Rout·Bout A228, A249, A250, A251 G:A6 G:A6 G:A6
2qbh A1565 Pout·Rout·Bout A1707, A1708, A1709, A1710, A1711, A1712 G:A727 C:A853 G:A727
2qou A1566 Pout·Rout·Bout A2011, A2012, A2013, A2014, A2015, A2016 A:A1357 A:A1254 C:A1359
2qou A1579 Pout·Rout·Bout A2074, A2075, A2076, A2077, A2078, A2079 U:A916 U:A13 G:A917
2qp0 A1592 Pout·Rout·Bout A2122, A2123, A2124, A2125, A2126, A2127 A:A1357 A:A1254 C:A1359
3v26 A1731 Pout·Rout·Bout A2035, A2036, A2037, A2038, A2039, A2040 A:A915 U:A13 G:A916
3v2d A3608 Pout·Rout·Bout A5412, A5413, A5414, A5415 A:A1762 G:A1681 U:A1757
4bpe A5066 Pout·Rout·Bout A2425, A2426, A2429, A2449, A2450, A2471 U:A1529 G:A1531 G:A1531
4bpe A5020 Pout·Rout·Bout A2034, A2035, A2036, A2058, A2059, A2269 A:A101 A:A100 U:A297
4bpe A5026 Pout·Rout·Bout A2037, A2057, A2067, A2278, A2279, A2280 A:A104 G:A374 U:A294
4bpn A5026 Pout·Rout·Bout A6439, A6440, A6441, A6442, A6443, A6444 A:A104 G:A374 U:A294
4bpn A5066 Pout·Rout·Bout A6528, A6529, A6530, A6531, A6532, A6534 U:A1529 G:A1531 G:A1531
4bpn A5077 Pout·Rout·Bout A6606, A6607, A6608, A6609, A6610, A6611 U:A1275 U:A1277 U:A1277
4bpn A5056 Pout·Rout·Bout A6201, A6202, A6203, A6204, A6205, A6206 G:A1113 U:A8 G:A1113
4bpn A5020 Pout·Rout·Bout A6401, A6403, A6404, A6405, A6406, A6407 A:A101 A:A100 U:A297
4bpo A5066 Pout·Rout·Bout A2285, A2286, A2287, A2444, A2445, A2446 U:A1529 G:A1531 G:A1531
4bpo A5020 Pout·Rout·Bout A2035, A2036, A2037, A2057, A2356, A2357 A:A101 A:A100 U:A297
4bpo A5026 Pout·Rout·Bout A2038, A2039, A2056, A2065, A2365, A2366 A:A104 G:A374 U:A294
4bpp A5020 Pout·Rout·Bout A7331, A7332, A7333, A7334, A7335, A7336 A:A101 A:A100 U:A297
4bpp A5026 Pout·Rout·Bout A7427, A7428, A7429, A7430, A7431, A7432 A:A104 G:A374 U:A294
4bpp A5066 Pout·Rout·Bout A8067, A8068, A8069, A8070, A8071, A8072 U:A1529 G:A1531 G:A1531
4bpp A5056 Pout·Rout·Bout A7907, A7908, A7909, A7910, A7911, A7912 G:A1113 U:A8 G:A1113
4dr2 A1747 Pout·Rout·Bout A2372, A2373, A2374, A2375, A2376 G:A666 A:A665 G:A667
4dr3 A1719 Pout·Rout·Bout A2111, A2112, A2113, A2114 A:A1004 U:A1025 G:A1024
4dv3 A1851 Pout·Rout·Bout A2229, A2230, A2231, A2232, A2233, A2234 G:A1224 C:A1223 A:A977

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>