MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4m:A1592, See in JSmolClick on the image to toggle views Site type: Pout Schematic drawing for Pout List of all 94 Mg2+ binding sites with the site type Pout 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 4a1e 06 Pout 05059, 05060, 05061, 05062, 05063, 05064 U:2140 4a1a 054 Pout 05427, 05428, 05429, 05430, 05431, 05432 U:258 4a1c 054 Pout 05251, 05252, 05253, 05254, 05255, 05256 U:258 4a1e 054 Pout 05459, 05460, 05461, 05462, 05463, 05464 U:258 4a17 055 Pout 05539, 05540, 05541, 05542, 05543, 05544 G:259 4a1e 055 Pout 05475, 05476, 05477, 05478, 05479, 05480 G:259 4a1a 055 Pout 05443, 05444, 05445, 05446, 05447, 05448 G:259 4a17 070 Pout 05699, 05700, 05701, 05702, 05703, 05704 A:25 4a1e 070 Pout 05635, 05636, 05637, 05638, 05639, 05640 A:25 4a1e 079 Pout 05715, 05716, 05717, 05718, 05719, 05720 A:24 4a17 079 Pout 05811, 05812, 05813, 05814, 05815, 05816 A:24 4lf9 S101 Pout A1831, A1832, A1833, S201, S202, S203 U:A1313 3v27 8101 Pout 8203, 8204, 8205, 8206, 8207 A:A631 3v27 0101 Pout A4640, A4641, 0206, 0207, 0208 C:A2263 4a1a 0199 Pout 06611, 06612, 06613, 06614, 06615, 06616 A:381 4a1e 0199 Pout 06755, 06756, 06757, 06758, 06759, 06760 A:381 4a17 0199 Pout 06979, 06980, 06981, 06982, 06983, 06984 A:381 4dv2 J201 Pout A2233, J301, J302, N202, N203, N204 C:A1189 4dv0 J202 Pout A2229, I201, J301, J302, J303, N201 C:A1189 4ji1 H202 Pout A2302, A2303, A2304, A2305, H301, H302 U:A5 4a1e 0366 Pout 08355, 08356, 08357, 08358, 08359, 08360 G:234 2nug A506 Pout C520, C521, A526, A527, A528, A529 C:C7 2nug B512 Pout D518, D519, D563, B527, B528, B529 C:D7 2c0b L1510 Pout L2023, L2024, L2028, L2029, R2002, R2003 A:R9 2bx2 L1511 Pout L2021, L2022, L2032, L2033, R2002, R2003 U:R12

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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