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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 5 of 18 | | | 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
1vs8 B2990 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3423, B3424, B3425 U:B741
1vs8 B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3417, B3418, B3419 A:B1783
1vt2 A2935 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3190, A3191, A3192
1w2b 03919 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 07079, 07085, 07088 G:01837 A:01839
1yhq 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04108, 08294, 08295 G:01837 A:01839
1yhq 08006 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 04125, 08287, 08367 G:02466
1yi2 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03358, 07727, 09006 G:0833
1yi2 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03627, 07731, 07814 G:02466, C:0920
1yi2 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 04094, 09613
1yi2 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03609, 07738, 07739 G:01837 A:01839
1yij 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03639, 07743, 07827 G:02466, C:0920
1yij 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03621, 07750, 07751 G:01837 A:01839
1yij 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03367, 07739, 09006 G:0833
1yij 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 04112, 09615
1yj9 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03171, 07552, 08828 G:0833
1yj9 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03444, 07556, 07637 G:02466, C:0920
1yj9 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03426, 07563, 07564 G:01837 A:01839
1yj9 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 03919, 09431 U:01422
1yjn 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03366, 07751, 09006 G:0833
1yjn 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03641, 07755, 07840 G:02466
1yjn 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03622, 07762, 07763 G:01837 A:01839
1yjn 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 04114, 09614
1yjw 78008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 06154, 06155, 09018 G:02466
1yjw 78005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 07931, 07933, 07942 G:01837 A:01839
2avy A1594 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1849, A1850, A1851 A:A288 G:A117, U:A118

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>