Sodium in PDB 8u5r: Structure of Mango II Variant Aptamer Bound to T01-6A

The structure of Structure of Mango II Variant Aptamer Bound to T01-6A, PDB code: 8u5r was solved by L.F.M.Passalacqua, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.80 / 2.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	36.929, 180.748, 106.248, 90, 90, 90
R / Rfree (%)	20 / 23.9

The structure of Structure of Mango II Variant Aptamer Bound to T01-6A also contains other interesting chemical elements:

Potassium

(K)

12 atoms

The binding sites of Sodium atom in the Structure of Mango II Variant Aptamer Bound to T01-6A (pdb code 8u5r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Mango II Variant Aptamer Bound to T01-6A, PDB code: 8u5r:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Mango II Variant Aptamer Bound to T01-6A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Mango II Variant Aptamer Bound to T01-6A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:35.1 occ:1.00 O A:HOH221 2.6 39.0 1.0 O A:HOH212 2.7 30.5 1.0 OP1 A:A30 2.8 32.3 1.0 N7 A:G31 3.0 30.9 1.0 N2 A:G7 3.1 26.2 1.0 O A:HOH207 3.1 26.1 1.0 OP2 A:G10 3.1 29.0 1.0 C8 A:G31 3.9 30.0 1.0 C5 A:G31 4.0 29.0 1.0 P A:A30 4.0 28.6 1.0 O6 A:G31 4.1 29.9 1.0 C2 A:G7 4.2 24.1 1.0 P A:G10 4.3 31.1 1.0 N7 A:A30 4.3 29.2 1.0 O3' A:A9 4.4 28.9 1.0 C6 A:G31 4.4 28.8 1.0 N1 A:G7 4.4 22.9 1.0 O5' A:A30 4.5 30.9 1.0 C8 A:A30 4.5 29.9 1.0 C2' A:A9 4.6 28.0 1.0 OP2 A:A30 4.6 25.2 1.0 O5' A:G10 4.7 30.6 1.0 C3' A:A9 4.7 30.1 1.0

Sodium binding site 2 out of 3 in the Structure of Mango II Variant Aptamer Bound to T01-6A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Mango II Variant Aptamer Bound to T01-6A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:49.3 occ:1.00 OP2 A:U12 2.6 46.5 1.0 O3' A:A28 3.4 46.7 1.0 OP2 A:G11 3.4 51.3 1.0 C8 A:G29 3.4 25.2 1.0 OP2 A:G29 3.5 48.8 1.0 O5' A:G11 3.6 46.9 1.0 P A:U12 3.8 42.9 1.0 O5' A:G29 3.9 35.5 1.0 P A:G29 3.9 36.4 1.0 O2' A:G10 4.0 29.3 1.0 C3' A:G11 4.1 34.0 1.0 N7 A:G29 4.1 23.7 1.0 P A:G11 4.2 42.2 1.0 C2' A:G29 4.2 36.4 1.0 O3' A:G11 4.2 45.0 1.0 OP1 A:U12 4.4 49.5 1.0 N9 A:G29 4.5 34.7 1.0 C1' A:A28 4.6 54.6 1.0 C5' A:G11 4.6 30.7 1.0 C3' A:A28 4.6 35.2 1.0 N2 A:G13 4.6 27.1 1.0 O2' A:G29 4.7 29.4 1.0 C8 A:G11 4.7 30.3 1.0 O4' A:A28 4.8 40.9 1.0 C4' A:A28 4.8 45.4 1.0 C1' A:G29 4.9 34.5 1.0 C4' A:G11 4.9 43.8 1.0 O2' A:A28 5.0 58.3 1.0

Sodium binding site 3 out of 3 in the Structure of Mango II Variant Aptamer Bound to T01-6A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Mango II Variant Aptamer Bound to T01-6A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na104 b:64.2 occ:1.00 O6 C:G7 2.6 63.0 1.0 C6 C:G7 3.7 55.4 1.0 O B:HOH205 4.1 38.0 1.0 C5 C:G7 4.4 58.4 1.0 N7 C:G7 4.4 59.9 1.0 OP1 C:A9 4.5 52.6 1.0 N1 C:G7 4.7 57.4 1.0 OP2 B:G15 4.8 50.0 1.0 OP1 B:G16 4.8 33.9 1.0

L.F.M.Passalacqua, A.R.Ferre-D'amare. Structure of Mango II Variant Aptamer Bound to T01-6A To Be Published.