MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df3:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·3Bout Schematic drawing for 2Pout·3Bout List of all 199 Mg2+ binding sites with the site type 2Pout·3Bout 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 8 of 8 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4bpo A5018 2Pout·3Bout A2010, A2011, A2013, A2016, A2124, A2125 G:A20, A:A19 G:A20, U:A21, A:A599 2qex 08071 2Pout·3Bout 03954, 05904, 07269, 07399, 07670, 07671 A:01815, C:01816 U:01813, C:01818, U:01817 1jj2 08071 2Pout·3Bout 03639, 05598, 06971, 07112, 07385, 07386 A:01815, C:01816 U:01813, C:01818, U:01817 1qvf 08071 2Pout·3Bout 03623, 05541, 06891, 07021, 07286, 07287 A:01815, C:01816 U:01813, C:01818, U:01817 1q7y A8071 2Pout·3Bout A3620, A5548, A6906, A7040, A7310, A7311 A:A1815, C:A1816 U:A1813, C:A1818, U:A1817 1m90 A8071 2Pout·3Bout A3642, A5592, A6955, A7096, A7368, A7369 A:A1815, C:A1816 U:A1813, C:A1818, U:A1817 1yij 08071 2Pout·3Bout 04127, 06056, 07408, 07537, 07808, 07809 A:01815, C:01816 U:01813, C:01818, U:01817 2otl 08071 2Pout·3Bout 04130, 06070, 07417, 07550, 07818, 07819 A:01815, C:01816 U:01813, U:01817, C:01818 1kc8 A8071 2Pout·3Bout A4116, A6051, A7425, A7561, A7837, A7838 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1k73 A8071 2Pout·3Bout A4108, A6060, A7436, A7573, A7849, A7850 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1yjn 08071 2Pout·3Bout 04128, 06069, 07418, 07549, 07821, 07822 A:01815, C:01816 U:01813, C:01818, U:01817 1kd1 A8071 2Pout·3Bout A4105, A6048, A7421, A7555, A7835, A7836 A:A1815, C:A1816 U:A1813, C:A1818, U:A1817 1q82 A8071 2Pout·3Bout A3624, A5539, A6901, A7035, A7310, A7311 A:A1815, C:A1816 U:A1817, C:A1818, U:A1813 1k9m A8071 2Pout·3Bout A4107, A6058, A7434, A7571, A7848, A7849 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1q86 A8071 2Pout·3Bout A3641, A5571, A6936, A7066, A7340, A7341 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 3cxc 08071 2Pout·3Bout 05058, 06967, 08456, 08730, 08731, 08933 A:01815, C:01816 U:01817, U:01813, C:01818 1vq4 08071 2Pout·3Bout 04424, 06318, 07618, 07743, 08065, 08066 A:01815, C:01816 U:01813, C:01818, U:01817 1k8a A8071 2Pout·3Bout A3699, A5624, A6978, A7112, A7387, A7388 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1s72 08071 2Pout·3Bout 03636, 05579, 06933, 07068, 07340, 07341 A:01815, C:01816 U:01813, C:01818, U:01817 1nji A8071 2Pout·3Bout A4103, A6053, A7417, A7553, A7830, A7831 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 1yi2 08071 2Pout·3Bout 04108, 06035, 07392, 07524, 07795, 07796 A:01815, C:01816 U:01813, C:01818, U:01817 1q81 A8071 2Pout·3Bout A3622, A5569, A6910, A7049, A7319, A7320 A:A1815, C:A1816 U:A1813, C:A1818, U:A1817 1m1k A8071 2Pout·3Bout A3708, A5657, A7015, A7150, A7426, A7427 A:A1815, C:A1816 U:A1813, U:A1817, C:A1818 2nz4 Q9007 2Pout·3Bout F33, F35, Q9013, Q9014, Q9015, Q9016 C:Q52, G:Q53 G:Q54, A:Q28, G:Q53

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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