Sodium in PDB 6e8s: Structure of the Imango-III Aptamer Bound to TO1-Biotin

The structure of Structure of the Imango-III Aptamer Bound to TO1-Biotin, PDB code: 6e8s 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)	38.33 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.031, 67.585, 76.667, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.8

The structure of Structure of the Imango-III Aptamer Bound to TO1-Biotin also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Potassium	(K)	2 atoms

The binding sites of Sodium atom in the Structure of the Imango-III Aptamer Bound to TO1-Biotin (pdb code 6e8s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Imango-III Aptamer Bound to TO1-Biotin, PDB code: 6e8s:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Imango-III Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Imango-III Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:73.2 occ:1.00 O A:HOH206 2.5 68.4 1.0 OP1 A:A12 2.7 73.4 1.0 O A:HOH203 2.7 73.8 1.0 O A:HOH204 2.9 76.6 1.0 N3 A:G9 2.9 66.1 1.0 O A:HOH209 3.1 69.3 1.0 O A:HOH201 3.2 77.0 1.0 O4' A:G9 3.2 73.4 1.0 O4' A:G10 3.3 73.7 1.0 C1' A:G9 3.5 69.1 1.0 N2 A:G9 3.7 61.3 1.0 C2 A:G9 3.7 66.5 1.0 C4 A:G9 3.8 65.2 1.0 N9 A:G9 4.0 68.1 1.0 C4' A:G9 4.1 74.2 1.0 O5' A:G10 4.2 80.2 1.0 P A:A12 4.2 79.0 1.0 C4' A:G10 4.2 71.9 1.0 C1' A:G10 4.3 70.7 1.0 O3' A:G9 4.3 81.7 1.0 N9 A:G10 4.4 64.9 1.0 O4 A:U24 4.5 67.3 1.0 C8 A:G10 4.5 68.0 1.0 OP1 A:G10 4.5 79.5 1.0 C5' A:G10 4.6 70.6 1.0 P A:G10 4.7 87.9 1.0 C5 A:U24 4.7 68.4 1.0 C3' A:A11 4.7 71.9 1.0 N7 A:A12 4.7 66.0 1.0 C3' A:G9 4.8 71.5 1.0 C2' A:G9 4.8 71.9 1.0 O5' A:A12 4.9 70.1 1.0 O3' A:A11 4.9 80.3 1.0 C4 A:U24 5.0 68.5 1.0

Sodium binding site 2 out of 4 in the Structure of the Imango-III Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Imango-III Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:79.2 occ:1.00 H92 B:SPM107 2.2 90.0 1.0 H111 B:SPM107 2.4 96.9 1.0 O2' B:A15 2.5 70.1 1.0 H131 B:SPM107 2.7 0.0 1.0 O3' B:A15 3.0 83.2 1.0 C9 B:SPM107 3.1 75.0 1.0 C11 B:SPM107 3.2 80.7 1.0 C13 B:SPM107 3.3 91.7 1.0 C2' B:A15 3.3 76.3 1.0 OP1 A:A21 3.4 71.0 1.0 H81 B:SPM107 3.5 88.8 1.0 HN41 B:SPM107 3.5 0.4 1.0 H82 B:SPM107 3.5 88.8 1.0 C1' B:A15 3.5 72.8 1.0 C5 A:U22 3.5 61.4 1.0 N14 B:SPM107 3.5 89.5 1.0 OP2 B:U16 3.6 88.6 1.0 C8 B:SPM107 3.6 74.0 1.0 C12 B:SPM107 3.6 87.3 1.0 H121 B:SPM107 3.6 0.8 1.0 N10 B:SPM107 3.7 93.5 1.0 C3' B:A15 3.7 77.1 1.0 H91 B:SPM107 3.8 90.0 1.0 C5' A:A21 3.8 76.1 1.0 P B:U16 3.8 84.8 1.0 H112 B:SPM107 4.0 96.9 1.0 O5' A:A21 4.0 70.0 1.0 O4 B:U17 4.1 73.1 1.0 H132 B:SPM107 4.2 0.0 1.0 N9 B:A15 4.3 70.2 1.0 P A:A21 4.4 71.6 1.0 C4 A:U22 4.4 67.5 1.0 O4 A:U22 4.4 63.1 1.0 C6 A:U22 4.4 64.1 1.0 HN42 B:SPM107 4.4 0.4 1.0 HN0 B:SPM107 4.4 0.2 1.0 OP1 B:U16 4.4 83.2 1.0 OP2 A:U22 4.5 64.2 1.0 H122 B:SPM107 4.5 0.8 1.0 O4' B:A15 4.6 77.3 1.0 C27 A:EKJ101 4.6 69.0 1.0 C4' B:A15 4.7 79.5 1.0 C26 A:EKJ101 4.8 61.7 1.0 C4' A:A21 4.8 67.8 1.0 C4 B:A15 4.9 64.2 1.0 C3' A:A21 4.9 72.8 1.0 N3 B:A15 5.0 71.5 1.0

Sodium binding site 3 out of 4 in the Structure of the Imango-III Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Imango-III Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na105 b:93.2 occ:1.00 OP2 B:U31 3.3 76.4 1.0 OP1 B:U31 3.7 81.6 1.0 P B:U31 4.0 75.0 1.0 OP2 B:C2 4.1 75.5 1.0 OP1 B:C2 4.2 84.5 1.0 OP2 B:U3 4.5 71.1 1.0 P B:C2 4.6 75.1 1.0

Sodium binding site 4 out of 4 in the Structure of the Imango-III Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Imango-III Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na106 b:85.1 occ:1.00 O B:HOH207 2.3 75.0 1.0 O B:HOH201 2.4 74.4 1.0 OP1 B:A12 2.6 85.4 1.0 O B:HOH202 2.7 80.5 1.0 N3 B:G9 2.9 72.0 1.0 O B:HOH203 3.1 81.6 1.0 O B:HOH206 3.1 76.6 1.0 O4' B:G10 3.3 79.9 1.0 O4' B:G9 3.5 75.9 1.0 C1' B:G9 3.7 79.3 1.0 N2 B:G9 3.7 66.3 1.0 C2 B:G9 3.7 71.6 1.0 C4 B:G9 3.8 70.5 1.0 P B:A12 4.1 89.1 1.0 N9 B:G9 4.1 73.9 1.0 O5' B:G10 4.3 84.0 1.0 C4' B:G10 4.3 81.3 1.0 C1' B:G10 4.3 76.3 1.0 O4 B:U24 4.3 73.5 1.0 C4' B:G9 4.4 77.1 1.0 N9 B:G10 4.5 73.0 1.0 N7 B:A12 4.6 69.1 1.0 O3' B:G9 4.6 89.0 1.0 C8 B:G10 4.7 70.8 1.0 C3' B:A11 4.7 91.6 1.0 C5' B:G10 4.7 79.3 1.0 C5 B:U24 4.8 72.6 1.0 O5' B:A12 4.8 82.0 1.0 OP1 B:G10 4.8 91.0 1.0 O3' B:A11 4.9 89.9 1.0 P B:G10 4.9 92.7 1.0 OP2 B:A12 4.9 84.9 1.0 C4 B:U24 4.9 71.5 1.0 N1 B:G9 5.0 68.6 1.0 C8 B:A12 5.0 72.4 1.0 C3' B:G9 5.0 82.4 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