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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
4tpf A3032 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3341, A3342, A3343 A:A2430
4tpf A3088 mer-3Oph A:A990(OP2), C:A991(OP2), G:A1186(OP2) A3596, A3597, A3598 G:A1185 G:A989, G:A1186
4tpf A3035 mer-3Oph C:A948(OP1), G:A962(OP1), U:A963(OP2) A3353, A3354, A3355 A:A947
4tpe A1603 mer-3Oph A:A116(OP1), G:A117(OP2), G:A289(OP2) A1711, A1712, A1713 A:A288 G:A117, U:A118
4tpe A1618 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1783, A1784, A1785 U:A571
4tpe A1640 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1884, A1885, A1886 C:A1501, G:A1504 U:A1506
4tpc A1622 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1802, A1803, A1804 C:A1501, G:A1504 U:A1506
4tpc A1641 mer-3Oph A:A116(OP1), G:A117(OP2), G:A289(OP2) A1886, A1887, A1888 A:A288 G:A117, U:A118
4tpb A3087 mer-3Oph A:A990(OP2), C:A991(OP2), G:A1186(OP2) A3593, A3594, A3595 G:A1185 G:A989, G:A1186
4tpb A3031 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3343, A3344, A3345 A:A2430
4tpa A1618 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1782, A1783, A1784 U:A571
4tpa A1603 mer-3Oph A:A116(OP1), G:A117(OP2), G:A289(OP2) A1711, A1712, A1713 A:A288 G:A117, U:A118
4tpa A1640 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1884, A1885, A1886 C:A1501, G:A1504 U:A1506
4tp9 A3088 mer-3Oph A:A990(OP2), C:A991(OP2), G:A1186(OP2) A3600, A3601, A3602 G:A1185 G:A1186, G:A989
4tp8 A1608 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1735, A1736, A1737 U:A571
4tp8 A1641 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1887, A1888, A1889 A:A288 G:A117, U:A118
4tp8 A1622 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1801, A1802, A1803 C:A1501, G:A1504 U:A1506
4tp7 A3032 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3338, A3339, A3340 A:A2430
4tp7 A3035 mer-3Oph C:A948(OP1), G:A962(OP1), U:A963(OP2) A3350, A3351, A3352 A:A947
4tp7 A3088 mer-3Oph A:A990(OP2), C:A991(OP2), G:A1186(OP2) A3593, A3594, A3595 G:A989, G:A1186
4tp6 A1603 mer-3Oph A:A116(OP1), G:A117(OP2), G:A289(OP2) A1711, A1712, A1713 A:A288 G:A117, U:A118
4tp6 A1640 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1884, A1885, A1886 C:A1501, G:A1504 U:A1506
4tp4 A1640 mer-3Oph A:A116(OP1), G:A117(OP2), G:A289(OP2) A1885, A1886, A1887 G:A117, U:A118
4tp4 A1621 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1801, A1802, A1803 C:A1501, G:A1504 U:A1506
4tp3 A3087 mer-3Oph A:A990(OP2), C:A991(OP2), G:A1186(OP2) A3593, A3594, A3595 G:A1185 G:A989, G:A1186

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>