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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 3 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
1q86 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3155, A7275, A7359 G:A2466, G:A2293
1qvf 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 03609, 09133
1qvf 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03147, 07224, 07304 G:02466
1qvf 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 07221, 08527, 09876 G:0833
1qvg 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03117, 07164, 07165 G:01837 A:01839
1qvg 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03134, 07157, 07237 G:02466, C:0920
1s72 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03134, 07283, 07284 G:01837 A:01839
1s72 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 07272, 08528, 09879 G:0833
1s72 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 03622, 09131
1s72 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03151, 07276, 07359 G:02466, G:02293
1vq4 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03665, 07936, 09328 G:0833
1vq4 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03915, 07947, 07948 G:01837 A:01839
1vq4 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03934, 07940, 08130 G:02466, C:0920
1vq4 08118 mer-3Oph A:02637(OP1), DA:4176(OP1), C:4175(OP1) 08185, 08186, 08187 U:02620, C:02636 A:02474
1vq5 48118 mer-3Oph A:02637(OP1), A:4176(OP1), C:4175(OP1) 08230, 47901, 47902 U:02620, C:02636 A:02474
1vq5 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 04413, 09935 U:01422
1vq5 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03945, 07985, 08174 G:02466, G:02293
1vq5 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03676, 07981, 09328 G:0833
1vq5 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03927, 07992, 07993 G:01837 A:01839
1vq6 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03937, 07949, 08138 G:02466, C:0920
1vq6 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03919, 07956, 07957 G:01837 A:01839
1vq6 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03664, 07945, 09328 G:0833
1vq6 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 04404, 09932 U:01422
1vq7 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 04424, 09933
1vq7 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03935, 07987, 07988 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>