MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbg:B2955, See in JSmolClick on the image to toggle views Site type: trans,trans-4Oph Schematic drawing for trans,trans-4Oph List of all 35 Mg2+ binding sites with the site type trans,trans-4Oph 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3iin B1 trans,trans-4Oph C:B88(OP1), G:B170(OP1), A:B172(OP1), DA:C207(OP2) DT:D3(O3') 1x8w B2 trans,trans-4Oph A:B184(OP1), A:B186(OP1), A:B187(OP2), G:B188(OP2) 2r8s R1002 trans,trans-4Oph A:R184(OP1), A:R186(OP1), A:R187(OP2), G:R188(OP2) R1008, R1009 A:R183 3r8t A2943 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3257, A3258 3oat A2943 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3220, A3221 3i1r A2944 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3228, A3229 2qoz B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3695, B3696 3ofr A2944 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3225, A3226 2qbi B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3201, B3202 1vs6 B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3205, B3206 2i2t B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3211, B3212 2aw4 B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3201, B3202 3i1n A2944 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3231, A3232 3r8s A2944 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3284, A3285 3i20 A2944 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3229, A3230 2z4l B2945 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3201, B3202 3i1t A2946 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3239, A3240 1vs8 B2954 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3255, B3256 2qbg B2955 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3262, B3263 2i2v B2955 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3268, B3269 2awb B2955 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3259, B3260 2qp1 B2955 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3765, B3766 2qbk B2955 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3258, B3259 2z4n B2956 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3261, B3262 4kix A3040 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3380, A3381

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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