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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 5 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
3cc2 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03176, 07404, 07405, 08769 A:0882, C:0884 U:0883, A:01836
3cc2 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03175, 07350, 08527, 08545 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
3cc2 08052 trans-2Oph U:01125(OP1), G:992(OP1) 03177, 07452, 98390, 98416 C:01126 C:01129, G:990
3cc7 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03655, 07838, 09012, 09030 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
3cce 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03643, 07813, 09029, 18953 G:01688 A:0844, A:01689, C:01690, C:01692, A:0882
3ccj 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03617, 07701, 09012, 09032 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
3ccl 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03646, 07817, 09031, 18953 G:01688 A:0844, A:01689, C:01690, C:01692, A:0882
3ccm 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03650, 07822, 09013, 09031 G:01688 A:0844, A:0882, A:01689, C:01690, C:01692
3ccq 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03643, 07838, 09013, 09032 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
3ccr 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03628, 07783, 09012, 09032 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
3ccs 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03622, 07792, 09013, 09030 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
3ccu 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03636, 07822, 09028, 18953 G:01688 A:0844, A:01689, C:01690, C:01692, A:0882
3ccv 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03630, 07797, 09027, 18953 G:01688 A:0844, A:01689, C:01690, C:01692, A:0882
3cd6 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03649, 07833, 09030, 18953 G:01688 A:0844, A:01689, C:01690, C:01692, A:0882
3cpw 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 04061, 08218, 09520, Z8953 G:01688 A:0844, A:01689, C:01690, C:01692, A:0882
3cxc 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03004, 03021, 04570, 08683 G:01688 A:0882, C:01692, A:0844, A:01689, C:01690
3cxc 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03227, 04571, 08736, 08737 A:0882, C:0884 U:0883, A:01836
3cxc 98052 trans-2Oph U:01125(OP1), G:93092(OP1) 04572, 04806, 08783, 98390 C:01126 C:01129, G:93090
3df2 B3326 trans-2Oph A:B751(OP1), A:B1614(OP1) B4327, B4328, B4329, B4330 A:B1614, C:B1615, C:B1617, A:B789
3df4 B3087 trans-2Oph U:B999(OP2), C:B1153(OP2) B4088, B4089, B4090, B4091 C:B998 G:B1154
3df4 B3327 trans-2Oph A:B751(OP1), A:B1614(OP1) B4328, B4329, B4330, B4331 A:B1614, C:B1615, C:B1617, A:B751, A:B789
3df4 B3579 trans-2Oph C:B787(OP1), U:B790(OP2) B4580, B4581, B4582, B4583 C:B791 A:B1780
3hhn C1021 trans-2Oph C:C70(OP1), U:C106(OP1) C1037, C1038, C1039, C1040 G:C72 A:C71
3hhn E1021 trans-2Oph C:E70(OP1), U:E106(OP1) E1039, E1040, E1041, E1042 G:E72 A:E71
3i1n A2994 trans-2Oph A:A1359(OP1), G:A1360(OP2) A3463, A3464, A3465, A3466 G:A1361

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>