Sodium in PDB 7p8z: Short Wilavidin Biotin Complex

The structure of Short Wilavidin Biotin Complex, PDB code: 7p8z was solved by O.Avraham, O.Livnah, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.79 / 1.67
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.555, 67.384, 77.789, 90, 90, 90
R / Rfree (%)	18.9 / 25.1

The binding sites of Sodium atom in the Short Wilavidin Biotin Complex (pdb code 7p8z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Short Wilavidin Biotin Complex, PDB code: 7p8z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Short Wilavidin Biotin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Short Wilavidin Biotin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na203 b:41.7 occ:1.00 O7 C:P33202 2.6 32.3 1.0 C11 C:P33202 2.6 32.5 1.0 O1 C:P33202 2.8 21.8 1.0 O4 C:P33202 3.0 26.1 1.0 O19 C:P33202 3.1 36.2 1.0 O16 C:P33202 3.2 30.8 1.0 C9 C:P33202 3.3 25.0 1.0 O10 C:P33202 3.4 33.2 1.0 C8 C:P33202 3.4 29.2 1.0 C17 C:P33202 3.5 29.4 1.0 C5 C:P33202 3.5 27.7 1.0 O13 C:P33202 3.5 34.0 1.0 C6 C:P33202 3.5 27.3 1.0 C12 C:P33202 3.5 29.0 1.0 C15 C:P33202 3.6 28.9 1.0 C14 C:P33202 3.6 24.3 1.0 O22 C:P33202 3.7 35.8 1.0 C21 C:P33202 3.7 36.0 1.0 C18 C:P33202 3.8 33.7 1.0 C2 C:P33202 3.9 19.3 1.0 C3 C:P33202 3.9 18.8 1.0 C20 C:P33202 4.0 34.1 1.0 CG1 C:VAL58 4.3 16.3 1.0 O C:GLY60 4.6 15.1 1.0

Sodium binding site 2 out of 2 in the Short Wilavidin Biotin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Short Wilavidin Biotin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na204 b:36.3 occ:1.00 O13 D:P33203 2.7 37.0 1.0 O7 D:P33203 2.8 31.0 1.0 O1 D:P33203 2.8 20.2 1.0 O10 D:P33203 3.0 26.9 1.0 O22 D:P33203 3.0 35.5 1.0 O4 D:P33203 3.2 24.2 1.0 C18 D:P33203 3.3 25.9 1.0 O19 D:P33203 3.4 36.5 1.0 C9 D:P33203 3.6 32.3 1.0 C12 D:P33203 3.6 29.3 1.0 C21 D:P33203 3.6 36.2 1.0 C11 D:P33203 3.6 29.2 1.0 C15 D:P33203 3.6 36.1 1.0 C5 D:P33203 3.7 28.6 1.0 C14 D:P33203 3.7 40.1 1.0 C17 D:P33203 3.7 29.4 1.0 O16 D:P33203 3.8 45.2 1.0 C8 D:P33203 3.8 34.4 1.0 C6 D:P33203 3.8 27.9 1.0 C20 D:P33203 3.9 32.0 1.0 C2 D:P33203 3.9 16.4 1.0 C3 D:P33203 4.0 14.4 1.0 CG1 D:VAL58 4.1 18.3 1.0 O D:GLY60 4.6 11.2 1.0

O.Avraham, E.A.Bayer, O.Livnah. Wilavidin* - A Novel Member of the Avidin Family That Forms Unique Biotin-Binding Hexamers. Febs J. 2021.
ISSN: ISSN 1742-464X
PubMed: 34726340
DOI: 10.1111/FEBS.16259