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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
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
2z4l B2989 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3408, B3409, B3410 U:B1781 A:B1783
2z4l B2965 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3297, B3298, B3299 A:B2430
2z4m A1545 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1610, A1611, A1612 U:A571
2z4m A1598 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1871, A1872, A1873 A:A288 G:A117, U:A118
2z4n B2991 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3423, B3424, B3425 U:B1781
2z4n B2993 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3429, B3430, B3431 U:B741
2z4n B2945 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3210, B3211, B3212 A:B2430
2z4n B3010 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3492, B3493, B3494
2z4n B2943 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3202, B3203, B3204 A:B947
2z75 B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A401, B402, B465 G:A1, A:B35
3b4a B201 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) A301, A302, B303 G:A3 G:A1, A:B35
3b4b B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B403, B404, B405 G:A1
3b4c B301 mer-3Oph C:A2(OP2), C:B36(OP2), G:B37(OP2) B402, A401 G:A1, A:B35
3cc2 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 07330, 08529, 09903 G:0833
3cc2 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 03657, 09146
3cc2 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03183, 07334, 07417 G:02466, G:02293
3cc2 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03165, 07341, 07342 G:01837 A:01839
3cc7 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03645, 07830, 07831 G:01837 U:01835 A:01839
3cc7 08006 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03664, 07823, 07905 G:02466, C:0920, G:02293
3cce 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03633, 07804, 07805 G:01837 U:01835 A:01839
3cce 08006 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03651, 07797, 07880 G:02466, C:0920
3ccj 08084 mer-3Oph C:01103(OP1), A:01106(OP2), A:01107(OP2) 07788, 07789, 07790 C:01104 A:01107
3ccl 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03635, 07807, 07808 G:01837 A:01839

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>