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

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Representative site 2qoy:A1566, See in JSmolMgRNA representative site for type 2PO-RO-BO      Click on the image to toggle views

Site type: 2Pout·Rout·Bout

Schematic drawing for

MgRNA type 2PO-RO-BO
List of all 32 Mg2+ binding sites with the site type 2Pout·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
1vs6 B2968 2Pout·Rout·Bout B3315, B3316, B3317, B3318, B3319, B3320 C:B1376, C:B1351 U:B1352 G:B1377
2a43 A207 2Pout·Rout·Bout A208, A209, A210, A211, A212, A213 A:A23, C:A22 G:A6 A:A23
2qan A2161 2Pout·Rout·Bout A2162, A2163, A2164, A2165, A2166, A2167 C:A726, G:A727 C:A853 G:A727
2qbb A2189 2Pout·Rout·Bout A2525, A2526, A2527, A2528, A2529, A2530 A:A768, C:A805 A:A767 G:A769
2qov B2908 2Pout·Rout·Bout B3032, B3033, B3034, B3035, B3036, B3037 C:B560, A:B1008 C:B1007 A:B1008
2qow A1591 2Pout·Rout·Bout A2120, A2121, A2122, A2123, A2124, A2125 G:A1356, A:A1357 A:A1254 C:A1359
2qoy A1566 2Pout·Rout·Bout A2013, A2014, A2015, A2016, A2017, A2018 A:A1357, G:A1356 A:A1254 C:A1359
2qoy A1565 2Pout·Rout·Bout A2007, A2008, A2009, A2010, A2011, A2012 C:A726, G:A727 C:A853 G:A727
2z4m A1569 2Pout·Rout·Bout A1731, A1732, A1733, A1734, A1735, A1736 C:A726, G:A727 C:A853 G:A727
3df1 A2143 2Pout·Rout·Bout A4144, A4145, A4146, A4147, A4148, A4149 A:A1357, G:A1356 A:A1254 C:A1359
3i1p A2933 2Pout·Rout·Bout A3179, A3180, A3181, A3182 U:A810, U:A811 G:A1252 A:A1253
3i1r A2960 2Pout·Rout·Bout A3302, A3303, A3304, A3305, A3306, A3307 A:A1936, G:A1959 A:A1936 G:A1959
3ofq A2989 2Pout·Rout·Bout A3439, A3440, A3441, A3442, A3443 A:A983, A:A572 G:A2029 U:A573
3ofr A2951 2Pout·Rout·Bout A3254, A3255, A3256, A3257, A3258 G:A1455, A:A1453 C:A1454 U:A1457
3ofz A2949 2Pout·Rout·Bout A3247, A3248, A3249, A3250, A3251 G:A1455, A:A1453 C:A1454 U:A1457
3v25 A3369 2Pout·Rout·Bout A3973, A3974, A3975, A3976, A3977 C:A2441, C:A2442 C:A2586 C:A2586
3v27 A3326 2Pout·Rout·Bout A3926, A3927, A3928, A3929, A3930, A3931 U:A464, G:A463 G:A1613 A:A789
3v29 A3410 2Pout·Rout·Bout A4064, A4065, A4066, A4067, 1104 G:A248, U:A387 G:A386 G:A386
3v29 A3512 2Pout·Rout·Bout A4439, A4440, A4441, A4442 U:A810, U:A811 C:A565 A:A1253
3v29 A3388 2Pout·Rout·Bout A3972, A3973, A3974, A3975, A3976 G:A1296, U:A1639 G:A2709 G:A2709
3v2c A1735 2Pout·Rout·Bout A2157, A2158, A2159, A2160, A2161 A:A915, G:A916 U:A13 G:A916
4bpo A5002 2Pout·Rout·Bout 52002, 52003, A2168, A2169, A2192, A2319 G:A920, A:A919 G:A1742 A:A1003
4bpp A5015 2Pout·Rout·Bout A7251, A7252, A7253, A7254, A7255, A7256 G:A1072, C:A608 U:A1071 C:A1068
4dh9 A1885 2Pout·Rout·Bout A2119, A2120, A2121, A2122, A2123 A:A915, G:A916 U:A13 G:A916
4dhc A3662 2Pout·Rout·Bout A4613, A4614, A4615, A4616, A4617, 1202 G:A248, U:A387 G:A386 G:A386

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>