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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"
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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
3oww A103 trans-2Oph A:A22(OP1), A:A75(OP2) A138, A139, A140, A141 C:A74 A:A75
3q3z A6 trans-2Oph U:A60(OP1), U:A66(OP1) A95, A96, A101, A102 A:A61
3q3z V83 trans-2Oph U:V60(OP1), U:V66(OP1) V171, V172, V173, V174 A:V61
3r8s A2982 trans-2Oph G:A370(OP2), A:A422(OP2) A3461, A3462, A3463, A3464 A:A423 U:A369 G:A370, A:A422, A:A423
3r8s A2926 trans-2Oph A:A751(OP1), A:A1614(OP1) A3208, A3209, A3210, A3211 G:A1613 A:A751, A:A789, C:A1617
3r8t A2937 trans-2Oph U:A999(OP2), C:A1153(OP2) A3229, A3230, A3231, A3232 C:A998 C:A1152
3v22 A1689 trans-2Oph G:A588(OP2), G:A644(OP1) A1874, A1875, A1876, A1877 C:A589, C:A645 G:A587
3v23 A3427 trans-2Oph A:A751(OP1), A:A1614(OP1) A4369, A4370, A4371, A4372 G:A1613 A:A751, A:A789, C:A1617, A:A1614
3v23 A3417 trans-2Oph A:A586(OP2), U:A1249(OP1) A4332, A4333, A4334 G:A585 U:A811
3v25 A3300 trans-2Oph U:A787(OP1), C:A790(OP2) A3748, A3749, A3750, A3751 A:A789, C:A791 A:A1780
3v25 A3302 trans-2Oph A:A586(OP2), U:A1249(OP1) A3755, A3756, A3757, A3758 C:A587, G:A585, G:A1250 U:A811
3v27 A3480 trans-2Oph A:A751(OP1), A:A1614(OP1) A4557, A4558, A4559, A4560 G:A1613 A:A751, A:A789, C:A1617, A:A1614
3v27 A3394 trans-2Oph G:A785(OP2), G:A792(OP2) A4201, A4202, A4203, A4204 C:A2440 G:A792
3v27 A3515 trans-2Oph C:A1298(OP2), U:A1639(OP2) A4703, A4704, A4705, A4706 C:A1297 C:A2710, C:A1638 G:A1299
3v27 A3471 trans-2Oph A:A586(OP2), U:A1249(OP1) A4514, A4515, A4516, A4517 G:A1250, G:A585 U:A811
3v29 A3414 trans-2Oph U:A787(OP1), C:A790(OP2) A4079, A4080, A4081, A4082 C:A791 C:A687
3v29 A3417 trans-2Oph A:A586(OP2), U:A1249(OP1) A4089, A4090, A4091, A4092 C:A587, G:A585, G:A1250 U:A811
3v29 A3389 trans-2Oph C:A1298(OP2), U:A1639(OP2) A3977, A3978, A3979, A3980 C:A1297 C:A1638 G:A1299
3v2c A1738 trans-2Oph A:A782(OP1), A:A794(OP1) A2166, A2167, A2168, A2169 C:A783 G:A1521, U:A1522, C:A1515 G:A1521
3v2d A3401 trans-2Oph A:A751(OP1), A:A1614(OP1) A4834, A4835, A4836, A4837 G:A1613 A:A751, C:A1617, A:A789, A:A1614
3v2d A3459 trans-2Oph C:A1298(OP2), U:A1639(OP2) A5010, A5011, A5012, A5013 C:A1638, C:A1297 C:A2710 G:A1299
3v2d A3224 trans-2Oph U:A2682(OP2), A:A2721(OP1) A4316, A4317, A4318, T301 C:A2683, G:A2722
3v2d A3400 trans-2Oph U:A787(OP1), C:A790(OP2) A4830, A4831, A4832, A4833 C:A791, A:A789 A:A1780
3v2d A3388 trans-2Oph A:A586(OP2), U:A1249(OP1) A4785, A4786, A4787, A4788 G:A1250, C:A587, G:A585
3v2d A3154 trans-2Oph U:A1352(OP2), C:A1376(OP2) A4115, A4116, A4117, A4118 C:A1351, C:A1375 G:A1377

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>