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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"
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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
2qbe B3141 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3727, B3728, B3729
2qbe B3484 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B4004, B4005, B4006 U:B1781 A:B1783
2qbe B3586 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B4083, B4084, B4085
2qbf A1559 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1680, A1681, A1682 C:A1501, G:A1504 U:A1506
2qbf A1544 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1609, A1610, A1611 U:A571 A:A574
2qbf A1597 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1873, A1874, A1875 G:A117, U:A118
2qbg B2944 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3211, B3212, B3213 A:B2430
2qbg B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3203, B3204, B3205
2qbg B3009 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3494, B3495, B3496
2qbg B2992 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3431, B3432, B3433 U:B741
2qbg B2990 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3425, B3426, B3427 A:B1783
2qbh A1595 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1852, A1853, A1854 A:A288 U:A118
2qbh A1546 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1621, A1622, A1623 U:A571
2qbi B2928 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3128, B3129, B3130
2qbi B2990 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3412, B3413, B3414 U:B741
2qbi B3009 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3484, B3485, B3486
2qbi B2964 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3295, B3296, B3297
2qbi B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3406, B3407, B3408 U:B1781 A:B1783
2qbj A1544 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1610, A1611, A1612 U:A571
2qbj A1597 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1870, A1871, A1872 A:A288 U:A118
2qbk B3009 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3487, B3488, B3489
2qbk B2992 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3427, B3428, B3429 U:B741
2qbk B2944 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3207, B3208, B3209 A:B2430
2qbk B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3199, B3200, B3201 A:B947
2qbk B2990 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3421, B3422, B3423 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>