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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
2qox B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3200, B3201, B3202
2qp1 B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3706, B3707, B3708 A:B947
2qbk B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3199, B3200, B3201 A:B947
2qbg B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3203, B3204, B3205
2awb B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3199, B3200, B3201 A:B947
2i2v B2942 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3209, B3210, B3211 A:B947
2z4n B2943 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3202, B3203, B3204 A:B947
2i2v B2944 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3217, B3218, B3219 A:B2430
2qbg B2944 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3211, B3212, B3213 A:B2430
2qp1 B2944 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3714, B3715, B3716 A:B2430
2qbk B2944 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3207, B3208, B3209 A:B2430
2z4n B2945 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3210, B3211, B3212 A:B2430
2qov B2964 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3299, B3300, B3301
2i2t B2964 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3305, B3306, B3307
2aw4 B2964 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3295, B3296, B3297
2qbi B2964 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3295, B3296, B3297
1vs6 B2964 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3299, B3300, B3301
2z4l B2965 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3297, B3298, B3299 A:B2430
3ofz A2987 mer-3Oph A:A990(OP2), C:A991(OP2), G:A1186(OP2) A3428, A3429, A3430 G:A1185 G:A1186
2qoz B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3900, B3901, B3902 A:B1783
1vs6 B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3410, B3411, B3412 A:B1783
2qov B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3410, B3411, B3412 U:B1781 A:B1783
1vs8 B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3417, B3418, B3419 A:B1783
2qbi B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3406, B3407, B3408 U:B1781 A:B1783
3ofc A2988 mer-3Oph A:A990(OP2), C:A991(OP2), G:A1186(OP2) A3439, A3440, A3441 G:A1185 G:A989

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>