MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs7:A1593, See in JSmolClick on the image to toggle views Site type: 2Pout Schematic drawing for 2Pout List of all 191 Mg2+ binding sites with the site type 2Pout 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 4qcz A3575 2Pout A4843, A4844, A4845, A4846 U:A869, G:A992 4too A3030 2Pout A3332, A3333, A3334, A3335, A3336, A3337 C:A965, A:A947 4too A3019 2Pout A3290, A3291, L202, L203 A:A621, G:A622 4tox A3137 2Pout A3805, A3806, A3807, A3808, A3809, N201 C:A2874, G:A2838 4tox A3020 2Pout A3292, A3293, A3294, L202 A:A621, G:A622 4tp3 A3042 2Pout A3386, A3387, T101, T102, T103 U:A1313, G:A1334 4tp3 A3077 2Pout A3547, A3548, S201, S202 A:A14, G:A15 4tp7 A3020 2Pout A3289, A3290, A3291, L202 A:A621, G:A622 4tp9 A3058 2Pout A3457, A3458, A3459, A3460, A3461, A3462 A:A1937, A:A1936 4tpb A3042 2Pout A3386, A3387, T101, T102, T103 U:A1313, G:A1334 4tpb A3136 2Pout A3802, A3803, A3804, A3805, A3806, N202 C:A2874, G:A2838 4tpb A3167 2Pout A3293, A3294, L301, L302 A:A621, G:A622 4tpb A3077 2Pout A3547, A3548, S201, S202 A:A14, G:A15 4tpd A3030 2Pout A3339, A3340, A3341, A3342, A3343, A3344 G:A822, A:A947 4tpf A3031 2Pout A3335, A3336, A3337, A3338, A3339, A3340 C:A965, A:A947 4tpf A3020 2Pout A3290, A3291, A3292, L202 A:A621, G:A622

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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