MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs8:B2932, See in JSmolClick on the image to toggle views Site type: 3Pout Schematic drawing for 3Pout List of all 207 Mg2+ binding sites with the site type 3Pout 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 6 of 9 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4tox A3031 3Pout A3336, A3337, A3338, A3339, A3340, A3341 G:A822, C:A965, A:A947 4tov A3031 3Pout A3337, A3338, A3339, A3340, A3341, A3342 G:A822, C:A965, A:A947 4tp9 A3031 3Pout A3338, A3339, A3340, A3341, A3342, A3343 G:A822, A:A947, C:A965 4peb A3034 3Pout A3360, A3361, A3362, A3363 U:A999, C:A1153, C:A998 3og0 A3035 3Pout A3636, A3637, A3638, A3639, A3640, N780 C:A2874, G:A2838, G:A2819 4tov A3036 3Pout A3357, A3358, A3359, A3360 U:A999, C:A1153, C:A998 3oas A3036 3Pout A3634, A3635, A3636, A3637, A3638, N780 C:A2874, G:A2819, G:A2838 3i22 A3036 3Pout A3635, A3636, A3637, A3638, A3639, N780 C:A2874, G:A2838, G:A2819 3ofd A3037 3Pout A3639, A3640, A3641, A3642, A3643, N780 C:A2874, G:A2819, G:A2838 3ofq A3037 3Pout A3637, A3638, A3639, A3640, A3641, N780 C:A2874, G:A2819, G:A2838 1vt2 A3037 3Pout A3645, A3646, A3647, A3648, A3649, N780 C:A2874, G:A2819, G:A2838 3i1p A3038 3Pout A3635, A3636, A3637, A3638, N777, N780 C:A2874, G:A2838, G:A2819 4tp3 A3039 3Pout A3378, A3379, A3380, A3381 A:A1268, C:A2006, G:A2048 4tpb A3039 3Pout A3378, A3379, A3380, A3381 A:A1268, C:A2006, G:A2048 3r8s A3040 3Pout A3711, A3712, A3713, A3714, A3715, N791 G:A2819, G:A2838, A:A2820 4tox A3043 3Pout A3385, A3386, A3387, T101, T102 U:A1313, G:A1334, C:A1335 4tpb A3056 3Pout A3450, A3451, A3452, A3453, C302 A:A1772, G:A1828, G:A1972 4tp3 A3058 3Pout A3460, A3461, A3462, A3463 G:A1973, G:A1972, G:A2592 4tpb A3058 3Pout A3460, A3461, A3462, A3463 G:A1972, G:A1973, G:A2592 4tp1 A3058 3Pout A3460, A3461, A3462, A3463, A3464, A3465 G:A1959, A:A1937, A:A1936 4peb A3061 3Pout A3484, A3485, A3486, A3487, A3488, A3489 U:A2613, A:A2051, G:A2578 4gar A3074 3Pout A3550, A3551, A3552, A3553 A:A2711, G:A2714, C:A2710 4tp3 A3076 3Pout A3543, A3544, A3545, A3546 A:A2711, G:A2714, C:A2710 4tp7 A3077 3Pout A3541, A3542, A3543, A3544 A:A2711, G:A2714, C:A2710 4pec A3085 3Pout A3589, A3590, A3591, A3592, A3593 A:A981, G:A978, C:A982

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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