MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2t:B2987, See in JSmolClick on the image to toggle views Site type: cis-2Oph·Ob Schematic drawing for cis-2Oph·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" Page 1 of 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3q3z V4 cis-2Oph·Ob A:V61(OP1), G:V62(OP2) U:V63(O4) V97, V98, V99 2zxu C79 cis-2Oph·Ob A:C7(OP1), A:C14(OP2) U:C8(O4) C112, C113 G:C15 3q3z A82 cis-2Oph·Ob A:A61(OP1), G:A62(OP2) U:A63(O4) A87, A89, A90 3v27 B215 cis-2Oph·Ob A:B57(OP2), A:B58(OP2) G:B23(O6) B316, B317, B318 G:B56 A:B59, C:B60, A:B58, U:B22 1ffk 02926 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 02930, 02931, 02932 U:0625 U:0626 1vs6 B2987 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3407, B3408, B3409 A:B2030 2aw4 B2987 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3403, B3404, B3405 A:B2030 2qbi B2987 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3403, B3404, B3405 U:B2500 U:B569, A:B2030 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 2qoz B2987 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3897, B3898, B3899 U:B2500 A:B2030 2i2t B2987 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3413, B3414, B3415 C:B2498 U:B569, A:B2030 1vs8 B2987 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3414, B3415, B3416 A:B2030 2i2v B2988 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3423, B3424, B3425 C:B2498 A:B2030 2awb B2988 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3415, B3416, B3417 A:B2030 2qox B2988 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3418, B3419, B3420 C:B2498 A:B2030 2z4l B2988 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3405, B3406, B3407 C:B2498 A:B2030 2qp1 B2989 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3926, B3927, B3928 C:B2498 A:B2030 2qbk B2989 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3418, B3419, B3420 C:B2498 A:B2030 2z4n B2990 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3420, B3421, B3422 C:B2498 A:B2030 2qox B2994 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B3437, B3438, B3439 G:B2608, G:B2583 2z4l B2994 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B3424, B3425, B3426 G:B2581 G:B2583, G:B2608 2qbg B2995 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B3441, B3442, B3443 G:B2581 G:B2583 2qbk B2995 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B3437, B3438, B3439 G:B2583 2z4n B2996 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B3439, B3440, B3441 G:B2583 3i1t A3005 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3515, A3516, A3517 U:A569, A:A2030

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].

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