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 1 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 1jj2 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03342, 09201 U:02586 1k73 A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3810, A9678 U:A2586 1kc8 A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3820, A9676 U:A2586 1kd1 A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3811, A9668 U:A2586 1kqs 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03325, 09190 1m1k A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3410, A9271 1m90 A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3345, A9197 U:A2586 1n8r A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3070, A4212 1nji A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3807, A9668 U:A2586 1q7y A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3324, A9195 U:A2586 1q81 A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3330, A9190 1q82 A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3326, A9189 U:A2586 1q86 A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3344, A9201 U:A2586 1qvf 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03329, 09199 U:02586 1s72 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03337, 09198 U:02586 1vq4 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 04120, 09994 U:02586 1vq5 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03003, 04131 U:02586 1vq6 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 04123, 09995 U:02586 1vq7 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 04139, 09998 U:02586 1vq9 08002 fac-3Oph·Ob A:02483(OP1), C:02534(OP1), U:02535(OP2) G:0627(O6) 08180, 09875 C:02071 1vqk 08002 fac-3Oph·Ob A:02483(OP1), C:02534(OP1), U:02535(OP2) G:0627(O6) 08323, 09888 C:02071 1vqo 08002 fac-3Oph·Ob A:02483(OP1), C:02534(OP1), U:02535(OP2) G:0627(O6) 08335, 09888 C:02071 1vs6 B2998 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3444, B3445 C:B2551 1vs8 B2998 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3449, B3450 C:B2551 1vw0 A3005 fac-3Oph·Ob A:A1669(OP2), C:A1670(OP2), G:A2550(OP1) U:A1671(O4)

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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