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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
2z4m A1545 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1610, A1611, A1612 U:A571
2z4l B2965 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3297, B3298, B3299 A:B2430
2z4l B2989 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3408, B3409, B3410 U:B1781 A:B1783
2z4l B2929 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3128, B3129, B3130
2z4l B3010 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3487, B3488, B3489
2z4k A1547 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1621, A1622, A1623 U:A571
2z4k A1596 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1856, A1857, A1858 A:A288 G:A117, U:A118
2qp1 B2944 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3714, B3715, B3716 A:B2430
2qp1 B3009 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3997, B3998, B3999
2qp1 B2990 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3929, B3930, B3931 A:B1783
2qp1 B2992 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3935, B3936, B3937 U:B741
2qp1 B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3706, B3707, B3708 A:B947
2qp0 A1544 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1890, A1891, A1892 U:A571
2qp0 A1577 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2052, A2053, A2054 A:A288 G:A117, U:A118
2qoz B2990 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3906, B3907, B3908 U:B741
2qoz B2928 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3623, B3624, B3625
2qoz B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3900, B3901, B3902 A:B1783
2qoy A1595 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2151, A2152, A2153 A:A288 G:A117, U:A118
2qoy A1546 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1916, A1917, A1918 U:A571
2qox B2991 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3427, B3428, B3429 U:B741
2qox B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3200, B3201, B3202
2qox B2989 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3421, B3422, B3423 U:B1781 A:B1783
2qow A1577 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2053, A2054, A2055 A:A288 G:A117, U:A118
2qov B2928 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3129, B3130, B3131
2qov B2964 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3299, B3300, B3301

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>