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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 6 of 18 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qal A2312 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2313, A2314, A2315 A:A288 G:A117, U:A118
2qb9 A2312 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2611, A2612, A2613 A:A288 G:A117, U:A118
3df1 A2312 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A4313, A4314, A4315 A:A288 G:A117, U:A118
2qan A2330 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2331, A2332, A2333 A:A288 G:A117, U:A118
2qbb A2330 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A2640, A2641, A2642 A:A288 G:A117, U:A118
3df3 A2330 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A4331, A4332, A4333 A:A288 G:A117, U:A118
2aw4 B2928 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3127, B3128, B3129
2qov B2928 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3129, B3130, B3131
2qbi B2928 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3128, B3129, B3130
1vs6 B2928 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3130, B3131, B3132 A:B947
2qoz B2928 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3623, B3624, B3625
2z4l B2929 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3128, B3129, B3130
3og0 A2933 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3188, A3189, A3190
3ofr A2934 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3182, A3183, A3184
3ofd A2934 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3188, A3189, A3190
3i20 A2934 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3186, A3187, A3188 A:A2430
3i22 A2934 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3190, A3191, A3192
3oas A2934 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3189, A3190, A3191
3i1r A2934 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3185, A3186, A3187 A:A2430
3i1p A2935 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3189, A3190, A3191
3i1t A2935 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3191, A3192, A3193 A:A2430
3ofq A2935 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3191, A3192, A3193
1vt2 A2935 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3190, A3191, A3192
3r8s A2937 mer-3Oph C:A948(OP1), G:A962(OP1), U:A963(OP2) A3253, A3254, A3255 A:A947
3ofr A2937 mer-3Oph C:A948(OP1), G:A962(OP1), U:A963(OP2) A3194, A3195, A3196 A:A947

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>