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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2i2t:B2987, See in JSmolMgRNA representative site for type cis-2OP-OB Click on the image to toggle views


Site type: cis-2Oph·Ob

Schematic drawing for
cis-2Oph·Ob
MgRNA type cis-2OP-OB
List of all 98 Mg2+ binding sites with the site type cis-2Oph·Ob 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
2qbg B2995 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B3441, B3442, B3443 G:B2581 G:B2583
2qbi B2987 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3403, B3404, B3405 U:B2500 U:B569, A:B2030
2qbk B2995 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B3437, B3438, B3439 G:B2583
2qbk B2989 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3418, B3419, B3420 C:B2498 A:B2030
2qex 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04176, 07588, 07589 U:02535 U:0625 U:0626
2qov B2987 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3407, B3408, B3409 C:B2498, U:B2500 U:B569, A:B2030
2qox B2994 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B3437, B3438, B3439 G:B2608, G:B2583
2qox B2988 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3418, B3419, B3420 C:B2498 A:B2030
2qoz B2987 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3897, B3898, B3899 U:B2500 A:B2030
2qp1 B2989 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3926, B3927, B3928 C:B2498 A:B2030
2z4l B2994 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B3424, B3425, B3426 G:B2581 G:B2583, G:B2608
2z4l B2988 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3405, B3406, B3407 C:B2498 A:B2030
2z4n B2996 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B3439, B3440, B3441 G:B2583
2z4n B2990 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3420, B3421, B3422 C:B2498 A:B2030
2zxu C79 cis-2Oph·Ob A:C7(OP1), A:C14(OP2) U:C8(O4) C112, C113 G:C15
3cc2 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 03887, 07318, 07319 U:02535 U:0625 U:0626
3cc4 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04380, 07827, 07828 C:02533, U:02535 U:0625 U:0626
3cc7 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04373, 07807, 07808 C:02533 U:0625 U:0626
3cce 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04350, 07781, 07782 C:02533, A:02535 U:0625 U:0626
3ccj 08002 cis-2Oph·Ob A:02483(OP1), U:02534(OP1) G:0627(O6) 04311, 07669, 07670 U:02535 U:0625 U:0626
3ccl 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04359, 07784, 07785 C:02533 U:0625 U:0626
3ccm 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04363, 07790, 07791 C:02533, U:02535 U:0625 U:0626
3ccq 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04356, 07806, 07807 U:02535 C:02533, U:0625 U:0626
3ccr 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04327, 07751, 07752 U:0625 U:0626
3ccs 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04343, 07759, 07760 C:02533, U:02535 U:0625 U:0626

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>