MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3r8s:A2932, See in JSmolClick on the image to toggle views Site type: Oph·Nb Schematic drawing for Oph·Nb List of all 134 Mg2+ binding sites with the site type Oph·Nb 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 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1yj9 08109 Oph·Nb U:0903(OP1) A:01357(N7) 03743, 05224, 05841, 09329 U:0904 G:0622, A:01356 1yjn 08109 Oph·Nb U:0903(OP1) A:01357(N7) 03943, 05415, 06048, 09513 U:0904 G:0622, A:01356 1yjw 78109 Oph·Nb U:0903(OP1) A:01357(N7) 06111, 06113, 06988, 06992 U:0904 A:01356 2aw4 B3013 Oph·Nb A:B1189(OP2) G:B1190(N7) B3504, B3505, B3506, B3507 U:B1188, G:B1190 2aw4 B2963 Oph·Nb U:B810(OP1) A:B1253(N7) B3291, B3292, B3293, B3294 C:B565, G:B1252 2awb B2948 Oph·Nb U:B810(OP1) A:B1253(N7) B3225, B3226, B3227, B3228 U:B811 C:B565 2i2t B3011 Oph·Nb U:B511(OP2) G:B512(N7) B3503, B3504, B3505 C:B510 2i2t B3013 Oph·Nb A:B1189(OP2) G:B1190(N7) B3512, B3513, B3514, B3515 U:B1188, G:B1190 2i2t B2963 Oph·Nb U:B810(OP1) A:B1253(N7) B3301, B3302, B3303, B3304 U:B811 C:B565 2i2v B2948 Oph·Nb U:B810(OP1) A:B1253(N7) B3235, B3236, B3237, B3238 U:B811 G:B1252 2i2v B3012 Oph·Nb A:B1189(OP2) G:B1190(N7) B3509, B3510, B3511, L1016 U:B1188, G:B1190 2otl 08110 Oph·Nb U:0903(OP1) A:01357(N7) 03937, 05423, 06050, 09512 U:0904 G:0622 2qam B3607 Oph·Nb A:B1189(OP2) G:B1190(N7) B4104, B4105, B4106, L610 U:B1188, G:B1190 2qam B3344 Oph·Nb U:B810(OP1) A:B1253(N7) B3892, B3893, B3894, B3895 U:B811 C:B565 2qao B3257 Oph·Nb U:B810(OP1) A:B1253(N7) B3830, B3831, B3832, B3833 U:B811 C:B565 2qao B3609 Oph·Nb A:B1189(OP2) G:B1190(N7) B4111, B4112, B4113, L146 U:B1188, G:B1190 2qba B3607 Oph·Nb A:B1189(OP2) G:B1190(N7) B4100, B4101, B4102, L610 U:B1188, G:B1190 2qba B3344 Oph·Nb U:B810(OP1) A:B1253(N7) B3889, B3890, B3891, B3892 U:B811 C:B565 2qbc B3609 Oph·Nb A:B1189(OP2) G:B1190(N7) B4111, B4112, B4113, L148 G:B1190 2qbc B3257 Oph·Nb U:B810(OP1) A:B1253(N7) B3830, B3831, B3832, B3833 U:B811 C:B565 2qbe B3344 Oph·Nb U:B810(OP1) A:B1253(N7) B3889, B3890, B3891, B3892 U:B811 C:B565 2qbe B3607 Oph·Nb A:B1189(OP2) G:B1190(N7) B4100, B4101, B4102, B4103 U:B1188, G:B1190 2qbf A1589 Oph·Nb U:A1224(OP1) A:A977(N1) A1834, A1835, A1836, A1837 G:A951, U:A952 C:A1223 2qbg B2948 Oph·Nb U:B810(OP1) A:B1253(N7) B3229, B3230, B3231, B3232 U:B811 C:B565 2qbg B3013 Oph·Nb A:B1189(OP2) G:B1190(N7) B3511, B3512, B3513, B3514 U:B1188, G:B1190

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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