MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vq7:08033, See in JSmolClick on the image to toggle views Site type: fac-3Oph·Ob Schematic drawing for fac-3Oph·Ob List of all 64 Mg2+ binding sites with the site type fac-3Oph·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 2 of 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1vy3 A3006 fac-3Oph·Ob A:A1669(OP2), C:A1670(OP2), G:A2550(OP1) U:A1671(O4) 1yi2 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03814, 09679 U:02586 1yij 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03827, 09680 U:02586 1yj9 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03631, 09500 U:02586 1yjn 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03833, 09682 U:02586 1yjw 78033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 07775, 09308 U:02586 2aw4 B2998 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3440, B3441 C:B2551 2i2t B2998 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3449, B3450 C:B2551 2i2v B2999 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3458, B3459 C:B2551 2otj 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03838, 09689 U:02586 2otl 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03827, 09679 2qam B3528 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B4041, B4042 2qao B3544 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B4060, B4061 C:B2551 2qba B3528 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B4038, B4039 2qbc B3544 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B4060, B4061 C:B2551 2qbe B3528 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B4037, B4038 2qbg B3000 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3459, B3460 C:B2551 2qbi B2998 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3439, B3440 2qbk B3000 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3454, B3455 C:B2551 2qex 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03644, 09501 2qov B2998 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3443, B3444 2qoz B2998 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3934, B3935 2qp1 B3000 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3963, B3964 C:B2551 2z4l B2999 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3441, B3442 2z4n B3001 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3457, B3458 C:B2551

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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