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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
2qao B3500 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B4026, B4027, B4028 U:B1781 A:B1783
2qao B3508 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B4032, B4033, B4034 U:B741
2qao B3588 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B4094, B4095, B4096
2qao B3235 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3812, B3813, B3814
2qao B3225 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3804, B3805, B3806 A:B947
2qb9 A2312 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2611, A2612, A2613 A:A288 G:A117, U:A118
2qb9 A2051 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A2401, A2402, A2403 C:A1501, G:A1504 U:A1506
2qb9 A2021 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A2376, A2377, A2378 U:A571
2qba B3484 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B4004, B4005, B4006 U:B1781 A:B1783
2qba B3141 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3726, B3727, B3728
2qba B3349 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3893, B3894, B3895
2qba B3586 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B4083, B4084, B4085
2qbb A2007 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A2375, A2376, A2377 U:A571
2qbb A2097 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A2447, A2448, A2449 C:A1501, G:A1504 U:A1506
2qbb A2330 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2640, A2641, A2642 A:A288 G:A117, U:A118
2qbc B3500 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B4026, B4027, B4028
2qbc B3225 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3804, B3805, B3806
2qbc B3235 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3812, B3813, B3814
2qbc B3588 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B4094, B4095, B4096
2qbc B3508 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B4032, B4033, B4034 U:B741
2qbd A2312 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2313, A2314, A2315 A:A288 G:A117, U:A118
2qbd A2051 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A2052, A2053, A2054 C:A1501, G:A1504 U:A1506
2qbd A2021 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A2022, A2023, A2024 U:A571
2qbe B3349 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3893, B3894, B3895
2qbe B3586 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B4083, B4084, B4085

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>