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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
2i2t B2990 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3422, B3423, B3424 U:B741
2i2u A1550 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1632, A1633, A1634 C:A1501 U:A1506
2i2u A1544 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1604, A1605, A1606 A:A574
2i2u A1572 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1737, A1738, A1739 A:A288 G:A117, U:A118
2i2v B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3209, B3210, B3211 A:B947
2i2v B2944 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3217, B3218, B3219 A:B2430
2i2v B2991 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3432, B3433, B3434 U:B741
2i2v B2989 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3426, B3427, B3428 U:B1781 A:B1783
2i2v B3008 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3492, B3493, B3494
2nz4 H9016 mer-3Oph C:H2(OP2), C:S29(OP2), G:S30(OP2) S9010, S9013, S9014 G:H1, A:S28
2otj 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03372, 07764, 09006
2otj 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03648, 07768, 07850 G:02466, G:02293
2otj 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03630, 07775, 07776 G:01837 A:01839
2otl 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03623, 07761, 07762 G:01837 A:01839
2otl 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03366, 07750, 09006 G:0833
2otl 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03641, 07754, 07837 G:02466, G:02293
2qal A2312 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2313, A2314, A2315 A:A288 G:A117, U:A118
2qal A2021 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A2022, A2023, A2024 U:A571
2qam B3492 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B4013, B4014, B4015 U:B741
2qam B3349 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3896, B3897, B3898
2qam B3484 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B4007, B4008, B4009 U:B1781
2qam B3586 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B4087, B4088, B4089
2qan A2007 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A2008, A2009, A2010 U:A571
2qan A2330 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2331, A2332, A2333 A:A288 G:A117, U:A118
2qan A2097 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A2098, A2099, A2100 C:A1501 U:A1506

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>