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

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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 3 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
2qbh A1550 2Pout·3Bout A1640, A1641, A1642, A1643, A1644, A1645 A:A315, A:A329 G:A319, A:A320, G:A318
2qbi B2957 2Pout·3Bout B3264, B3265, B3266, B3267, B3268, B3269 A:B616, G:B617 G:B617, G:B618, G:B619
2qbk B2939 2Pout·3Bout B3184, B3185, B3186, B3187, B3188, B3189 A:B447, U:B29 U:B29, G:B473, G:B474
2qex 08071 2Pout·3Bout 03954, 05904, 07269, 07399, 07670, 07671 A:01815, C:01816 U:01813, C:01818, U:01817
2qov B2957 2Pout·3Bout B3267, B3268, B3269, B3270, B3271, B3272 A:B616, G:B617 G:B619, G:B617, G:B618
2qov B2922 2Pout·3Bout B3097, B3098, B3099, B3100, B3101, B3102 U:B1267, A:B2009 G:B2010, U:B2011, A:B2009
2qox B2930 2Pout·3Bout B3139, B3140, B3141, B3142, B3143, B3144 A:B2453, C:B2452 A:B2453, A:B2497, G:B2454
2qox B2927 2Pout·3Bout B3123, B3124, B3125, B3126, B3127, B3128 A:B616, G:B617 G:B617, G:B618, G:B619
2qoz B2957 2Pout·3Bout B3758, B3759, B3760, B3761, E314, E3266 A:B616, G:B617 G:B617, G:B618, G:B619
2qp1 B2930 2Pout·3Bout B3645, B3646, B3647, B3648, B3649, B3650 A:B2453, C:B2452 A:B2453, A:B2497, G:B2454
2z4l B2958 2Pout·3Bout B3264, B3265, B3266, B3267, B3268, B3269 G:B617, A:B616 G:B617, G:B618, G:B619
2z4n B2928 2Pout·3Bout B3125, B3126, B3127, B3128, B3129, B3130 A:B616, G:B617 G:B617, G:B618, G:B619
2z4n B2960 2Pout·3Bout B3279, B3280, B3281, B3282, B3283, Q321 A:B582, A:B1253 A:B582, G:B583, G:B585
354d A203 2Pout·3Bout A315, A316, A317, A318, B313, B314 G:A75, A:B99 G:A75, G:A76, U:A77
3cxc 08071 2Pout·3Bout 05058, 06967, 08456, 08730, 08731, 08933 A:01815, C:01816 U:01817, U:01813, C:01818
3df1 A2031 2Pout·3Bout A4032, A4033, A4034, A4035, A4036, A4037 G:A645, U:A644 G:A645, U:A593, G:A646
3df2 B3457 2Pout·3Bout B4458, B4459, B4460, B4461, B4462, B4463 A:B2451, C:B2452 G:B2455, A:B2453, G:B2454
3df2 B3309 2Pout·3Bout B4310, B4311, B4312, B4313, B4314, B4315 A:B616, G:B617 G:B617, G:B619, G:B618
3df3 A2225 2Pout·3Bout A4226, A4227, A4228, A4229, A4230 U:A1348, A:A1349 G:A1371, U:A1372, G:A1370
3df3 A2016 2Pout·3Bout A4017, A4018, A4019, A4020, A4021, A4022 G:A803, U:A804 G:A773, G:A771, U:A772
3df4 B3337 2Pout·3Bout B4338, B4339, B4340, B4341, B4342, B4343 G:B2819, G:B1653 A:B2821, G:B2822, G:B2819
3df4 B3152 2Pout·3Bout B4153, B4154, B4155, B4156, B4157, B4158 A:B2453, C:B2452 A:B2453, A:B2497, G:B2454
3df4 B3133 2Pout·3Bout B4134, B4135, B4136, B4137, B4138, B4139 A:B616, G:B617 G:B618, G:B619, G:B617
3i1m A1537 2Pout·3Bout A1593, A1594, A1595, A1596, A1597, A1598 A:A415, G:A416 G:A417, G:A416, U:A426
3i1n A2921 2Pout·3Bout A3129, A3130, A3131, A3132, A3133, A3134 A:A616, A:A608 G:A617, G:A618, G:A619

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>