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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 1 of 18 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1hr2 A3 mer-3Oph A:A184(OP1), A:A186(OP1), A:A187(OP2) A325, A326, A327 A:A183, G:A188
1hr2 B4 mer-3Oph A:B184(OP1), A:B186(OP1), A:B187(OP2) B329, B330, B331 A:B183, G:B188
1jj2 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 07317, 08528, 09884 G:0833
1jj2 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03139, 07328, 07329 G:01837 A:01839
1jj2 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03156, 07321, 07404 G:02466, G:02293
1jj2 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 03625, 09133
1k73 A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A3355, A7781, A9006 G:A833
1k73 A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A4095, A9610
1k73 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3624, A7785, A7868 G:A2466, G:A2293
1k8a A8005 mer-3Oph A:A1836(OP1), U:A1838(OP1), A:A1839(OP2) A3202, A7329, A7330 G:A1837 A:A1839
1k8a A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A7319, A8609, A9946 G:A833
1k8a A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3220, A7323, A7406 G:A2466
1k9m A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A4093, A9605
1k9m A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A3351, A7778, A9006 G:A833
1k9m A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3621, A7782, A7867 G:A2466
1kc8 A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A4102, A9610
1kc8 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3634, A7771, A7856 G:A2466
1kc8 A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A3356, A7767, A9009 G:A833
1kd1 A8005 mer-3Oph A:A1836(OP1), U:A1838(OP1), A:A1839(OP2) A3607, A7775, A7776 G:A1837 A:A1839
1kd1 A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A3357, A7764, A9008
1kd1 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3625, A7768, A7854 G:A2466
1kqs 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03138, 07256, 07339 G:02466, C:0920
1kqs 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 03604, 09125
1kqs 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 07252, 08529, 09866 G:0833
1kqs 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03119, 07263, 07264 G:01837 A:01839

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>