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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 2 of 18 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1m1k A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A3694, A9205
1m1k A8005 mer-3Oph A:A1836(OP1), U:A1838(OP1), A:A1839(OP2) A3207, A7367, A7368 G:A1837 A:A1839
1m1k A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3224, A7360, A7445 G:A2466
1m1k A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A7356, A8606, A9956 G:A833
1m90 A8005 mer-3Oph A:A1836(OP1), U:A1838(OP1), A:A1839(OP2) A3140, A7310, A7311 G:A1837 A:A1839
1m90 A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A7299, A8528, A9883 G:A833
1m90 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3158, A7303, A7387 G:A2466, G:A2293
1n8r A8005 mer-3Oph A:A1836(OP1), U:A1838(OP1), A:A1839(OP2) A4007, A8263, A8264 G:A1837 A:A1839
1n8r A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A3748, A8252, A9410 G:A833
1n8r A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A4025, A8256, A8411 G:A2466, C:A920
1nji A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A4089, A9603
1nji A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A3353, A7759, A9007
1nji A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3623, A7763, A7849 G:A2466
1q7y A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A3605, A9127
1q7y A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3139, A7246, A7329 G:A2466, C:A920, G:A2293
1q81 A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A7250, A8528, A9870 G:A833
1q81 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3142, A7254, A7338 G:A2466
1q81 A8005 mer-3Oph A:A1836(OP1), U:A1838(OP1), A:A1839(OP2) A3123, A7261, A7262 G:A1837 A:A1839
1q81 A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A3609, A9123
1q82 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3142, A7244, A7328 G:A2466, C:A920
1q82 A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A3611, A9125
1q82 A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A7240, A8529, A9868 G:A833
1q86 A8005 mer-3Oph A:A1836(OP1), U:A1838(OP1), A:A1839(OP2) A3137, A7282, A7283 G:A1837 A:A1839
1q86 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3155, A7275, A7359 G:A2466, G:A2293
1q86 A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A7271, A8528, A9880 G:A833

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>