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

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Representative site 1vqo:08005, See in JSmolMgRNA representative site for type mer-3OP        Click on the image to toggle views


Site type: mer-3Oph

Schematic drawing for
mer-3Oph

MgRNA type mer-3OP
List of all 430 Mg2+ binding sites with the site type mer-3Oph 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 6 of 18 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2avy A1594 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1849, A1850, A1851 A:A288 G:A117, U:A118
2avy A1546 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1619, A1620, A1621 U:A571 A:A574
2aw4 B2928 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3127, B3128, B3129
2aw4 B2964 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3295, B3296, B3297
2aw4 B3009 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3487, B3488, B3489
2aw4 B2990 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3412, B3413, B3414 U:B741
2aw7 A1559 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1682, A1683, A1684 C:A1501, G:A1504 U:A1506
2aw7 A1598 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1875, A1876, A1877 A:A288 G:A117, U:A118
2aw7 A1544 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1610, A1611, A1612 U:A571 A:A574
2awb B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3199, B3200, B3201 A:B947
2awb B3013 mer-3Oph C:B1006(OP1), A:B1009(OP2), A:B1010(OP2) B3506, B3507, B3508 C:B1007 A:B1008 A:B1010
2awb B2991 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3424, B3425, B3426 U:B741
2awb B2989 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3418, B3419, B3420 U:B1779 A:B1783
2gcs B501 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B261, B288, B289 G:A1, A:B35
2gcv B401 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B282, B324, B325 G:A1, A:B35
2h0s B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A229, B220, B230 G:A1, A:B35
2h0w B501 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A282, A324, B325 G:A1, A:B35
2h0x B501 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B261, B288, B289 G:A1, A:B35
2ho6 B201 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A302, A303, B304 A:B35, G:A1
2i2p A1602 mer-3Oph G:A1494(OP2), U:A1495(OP2), U:X5(OP2) A1895, A1896, X363
2i2p A1595 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1858, A1859, A1860 A:A288 G:A117, U:A118
2i2p A1546 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1620, A1621, A1622 U:A571 A:A574
2i2t B2990 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3422, B3423, B3424 U:B741
2i2t B3009 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3495, B3496, B3497
2i2t B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3416, B3417, B3418 U:B1781 A:B1783

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>