Magnesium in PDB 6e8u: Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin

The structure of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin, PDB code: 6e8u was solved by R.J.Trachman, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.59 / 1.55
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.270, 53.270, 188.036, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.6

The structure of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin also contains other interesting chemical elements:

Potassium	(K)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin (pdb code 6e8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin, PDB code: 6e8u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:45.3 occ:1.00 O B:HOH227 1.9 41.1 1.0 O B:HOH307 2.0 51.5 1.0 O B:HOH267 2.0 33.6 1.0 OP1 B:G25 2.2 32.4 1.0 O B:HOH223 2.2 40.6 1.0 O B:HOH292 2.2 46.5 1.0 O B:HOH313 3.3 51.4 1.0 O B:HOH248 3.6 37.0 1.0 P B:G25 3.7 28.9 1.0 O B:HOH284 3.9 49.4 1.0 O B:HOH283 4.1 39.5 1.0 O B:HOH247 4.1 38.9 1.0 OP2 B:A6 4.2 35.0 1.0 O B:HOH290 4.2 44.6 1.0 C3' B:G24 4.3 23.0 1.0 O B:HOH262 4.3 41.5 1.0 O2' B:G23 4.3 26.9 1.0 O3' B:G24 4.4 26.8 1.0 OP2 B:G24 4.5 30.1 1.0 O5' B:G25 4.5 30.5 1.0 O B:HOH301 4.5 37.7 1.0 O3' B:G23 4.6 23.1 1.0 O B:HOH321 4.6 46.2 1.0 OP2 B:G25 4.7 33.5 1.0 O5' B:G24 4.7 25.9 1.0 P B:G24 5.0 25.5 1.0 OP2 B:A7 5.0 29.1 1.0

Magnesium binding site 2 out of 5 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:30.8 occ:1.00 O B:HOH275 2.0 32.6 1.0 OP2 B:G28 2.0 27.9 1.0 O B:HOH294 2.0 37.1 1.0 O B:HOH312 2.1 34.1 1.0 O B:HOH293 2.2 36.9 1.0 O4 B:U29 2.2 31.2 1.0 C4 B:U29 3.2 29.6 1.0 P B:G28 3.4 27.2 1.0 C5 B:U29 3.7 27.2 1.0 OP1 B:G28 3.9 29.3 1.0 O B:HOH273 4.0 33.1 1.0 O B:HOH208 4.2 49.1 1.0 O B:HOH319 4.2 48.1 1.0 O3' B:A27 4.2 27.3 1.0 O5' B:G28 4.4 24.8 1.0 N3 B:U29 4.4 26.2 1.0 C5' B:A27 4.6 37.5 1.0 C3' B:A27 4.7 25.8 1.0 O B:HOH253 4.7 35.0 1.0 C6 B:U29 5.0 23.9 1.0

Magnesium binding site 3 out of 5 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:31.4 occ:1.00 O B:HOH327 2.0 29.6 1.0 O B:HOH250 2.0 28.9 1.0 O B:HOH211 2.0 31.3 1.0 O B:HOH272 2.1 36.0 1.0 O B:HOH299 2.1 31.9 1.0 O B:HOH226 2.2 33.3 1.0 OP1 B:A11 3.9 35.6 1.0 O B:HOH204 4.2 37.9 1.0 N3 B:A7 4.2 30.1 1.0 O6 B:G23 4.2 28.9 1.0 O2' B:A7 4.2 31.1 1.0 O4' B:G8 4.3 28.6 1.0 N7 B:A11 4.3 28.8 1.0 N7 B:G23 4.4 22.7 1.0 N3 B:G8 4.4 23.9 1.0 C2' B:A7 4.5 25.5 1.0 C2 B:A7 4.6 31.5 1.0 C8 B:A11 4.7 27.1 1.0 C4 B:G8 4.9 24.9 1.0 C1' B:G8 4.9 25.4 1.0 C2 B:G8 5.0 22.1 1.0

Magnesium binding site 4 out of 5 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:41.7 occ:1.00 O B:HOH339 2.1 42.5 1.0 O B:HOH210 2.1 38.0 1.0 O B:HOH258 2.1 39.0 1.0 O B:HOH232 2.1 38.7 1.0 O B:HOH342 2.2 49.5 1.0 O B:HOH274 2.2 39.7 1.0 O B:HOH289 3.8 37.2 1.0 O4 B:U35 4.0 33.9 1.0 O6 B:G34 4.2 32.0 1.0 O4 B:U2 4.4 39.3 1.0 N7 B:G34 4.4 29.8 1.0 N6 B:A3 4.8 33.8 1.0 N4 B:C33 4.8 31.9 1.0 C6 B:G34 5.0 29.0 1.0

Magnesium binding site 5 out of 5 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:20.4 occ:0.50 OP1 B:U19 2.0 23.1 1.0 O B:HOH249 2.1 23.0 1.0 O B:HOH260 2.1 23.7 1.0 P B:U19 3.4 21.6 1.0 OP2 B:U19 4.1 23.6 1.0 O5' B:U19 4.2 20.3 1.0 N2 B:G28 4.3 21.3 1.0 N3 B:G28 4.3 21.7 1.0 N1 B:A27 4.4 22.9 1.0 O3' B:G18 4.5 21.2 1.0 O2' B:G28 4.5 22.0 1.0 O B:HOH266 4.6 24.2 1.0 C5 B:U19 4.7 26.9 1.0 C2 B:G28 4.8 23.1 1.0 C2 B:A27 4.8 21.5 1.0 C6 B:U19 5.0 26.8 1.0

R.J.Trachman 3Rd., A.Autour, S.C.Y.Jeng, A.Abdolahzadeh, A.Andreoni, R.Cojocaru, R.Garipov, E.V.Dolgosheina, J.R.Knutson, M.Ryckelynck, P.J.Unrau, A.R.Ferre-D'amare. Structure and Functional Reselection of the Mango-III Fluorogenic Rna Aptamer. Nat. Chem. Biol. V. 15 472 2019.
ISSN: ESSN 1552-4469
PubMed: 30992561
DOI: 10.1038/S41589-019-0267-9