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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3q3z:A6, See in JSmolMgRNA representative site for type trans-2OP Click on the image to toggle views


Site type: trans-2Oph

Schematic drawing for
trans-2Oph
MgRNA type trans-2OP
List of all 282 Mg2+ binding sites with the site type trans-2Oph 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 4 of 12 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qbe B3577 trans-2Oph C:B787(OP1), U:B790(OP2) B4076, B4077, B4078, B4079 A:B789, C:B791 A:B1780
2qbe B3326 trans-2Oph A:B751(OP1), A:B1614(OP1) B3877, B3878, B3879, B3880 G:B1613 A:B751, C:B1617, A:B1614, C:B1615, A:B789
2qbg B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3286, B3287, B3288, B3289 G:B1613 A:B751, C:B1617, A:B1614, C:B1615, A:B789
2qbg B3007 trans-2Oph C:B787(OP1), U:B790(OP2) B3487, B3488, B3489, B3490 A:B789 A:B1780
2qbg B2919 trans-2Oph U:B999(OP2), C:B1153(OP2) B3088, B3089, B3090, B3091 C:B1152, C:B998 G:B1154
2qbi B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3277, B3278, B3279, B3280 G:B1613 A:B751, A:B1614, C:B1617, C:B1615, A:B789
2qbi B3007 trans-2Oph C:B787(OP1), U:B790(OP2) B3477, B3478, B3479, B3480 C:B791 A:B1780
2qbk B3007 trans-2Oph C:B787(OP1), U:B790(OP2) B3480, B3481, B3482, B3483 C:B791 A:B1780
2qbk B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3282, B3283, B3284, B3285 G:B1613 A:B751, A:B1614, C:B1617, C:B1615, A:B789
2qbk B2919 trans-2Oph U:B999(OP2), C:B1153(OP2) B3087, B3088, B3089, B3090 C:B998 C:B1152 G:B1154
2qex 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03448, 07676, 07677, 09065 A:0882, C:0884 U:0883, C:0778
2qex 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03447, 07621, 08827, 08846 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
2qov B3007 trans-2Oph C:B787(OP1), U:B790(OP2) B3482, B3483, B3484, B3485 C:B791 A:B1780
2qox B2919 trans-2Oph U:B999(OP2), C:B1153(OP2) B3085, B3086, B3087, B3088 C:B998 G:B1154
2qox B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3283, B3284, B3285, B3286 A:B1614, C:B1615, C:B1617, A:B751, A:B789
2qox B3006 trans-2Oph C:B787(OP1), U:B790(OP2) B3482, B3483, B3484, B3485 C:B791 A:B1780
2qoz B2978 trans-2Oph G:B2061(OP2), G:B2502(OP2) B3854, B3855, B3856, B3857 G:B2446 A:B2060, G:B2502
2qoz B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3770, B3771, B3772, B3773 G:B1613 A:B1614, C:B1615, C:B1617, A:B789
2qp1 B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3789, B3790, B3791, B3792 G:B1613 A:B1614, C:B1615, C:B1617, A:B751, A:B789
2qp1 B3007 trans-2Oph C:B787(OP1), U:B790(OP2) B3990, B3991, B3992, B3993 A:B789 A:B1780
2qp1 B2919 trans-2Oph U:B999(OP2), C:B1153(OP2) B3592, B3593, B3594, B3595 C:B998 C:B1152 G:B1154
2z4l B2961 trans-2Oph A:B751(OP1), A:B1614(OP1) B3278, B3279, B3280, B3281 G:B1613 A:B751, A:B1614, G:B1613, C:B1617, C:B1615, A:B789
2z4l B3008 trans-2Oph C:B787(OP1), U:B790(OP2) B3480, B3481, B3482, B3483 C:B791 A:B1780
2z4n B3008 trans-2Oph C:B787(OP1), U:B790(OP2) B3485, B3486, B3487, B3488 C:B791 A:B1780
2z4n B2961 trans-2Oph A:B751(OP1), A:B1614(OP1) B3284, B3285, B3286, B3287 G:B1613 A:B751, A:B1614, C:B1615, A:B789

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>