Sodium in PDB 7zn1: Avidin + Biotin-Tempo

The structure of Avidin + Biotin-Tempo, PDB code: 7zn1 was solved by J.Milani, K.Lau, F.Pojer, J.P.Ansermet, F.Saenz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.50 / 2.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.353, 80.952, 60.951, 90, 119.08, 90
R / Rfree (%)	22.6 / 27.9

The structure of Avidin + Biotin-Tempo also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Avidin + Biotin-Tempo (pdb code 7zn1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Avidin + Biotin-Tempo, PDB code: 7zn1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Avidin + Biotin-Tempo


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Avidin + Biotin-Tempo within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:74.1 occ:1.00 O A:HOH310 2.1 63.1 1.0 OD2 A:ASP129 2.2 65.8 1.0 OD2 A:ASP132 2.6 67.8 1.0 OD1 A:ASP132 2.8 67.0 1.0 O A:HOH302 2.8 73.1 1.0 CG A:ASP132 3.0 65.1 1.0 CG A:ASP129 3.3 74.2 1.0 CB A:ASP129 3.9 69.3 1.0 OD1 A:ASP129 4.3 73.4 1.0 CB A:ASP132 4.6 57.2 1.0 NZ A:LYS135 4.9 68.2 1.0

Sodium binding site 2 out of 4 in the Avidin + Biotin-Tempo


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Avidin + Biotin-Tempo within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:59.5 occ:1.00 OD1 B:ASP129 2.3 65.9 1.0 OD2 B:ASP129 2.7 67.0 1.0 CG B:ASP129 2.8 62.9 1.0 OD1 B:ASP132 2.9 66.5 1.0 OD2 B:ASP132 3.3 67.3 1.0 CG B:ASP132 3.4 63.8 1.0 O B:HOH301 3.9 52.0 1.0 CB B:ASP129 4.2 51.7 1.0 N B:ASP129 4.6 64.5 1.0 CB B:ASP132 4.6 55.9 1.0 CB B:ASN128 5.0 64.8 1.0

Sodium binding site 3 out of 4 in the Avidin + Biotin-Tempo


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Avidin + Biotin-Tempo within 5.0Å range: probe atom residue distance (Å) B Occ C:Na204 b:57.0 occ:1.00 OD2 C:ASP129 2.2 61.4 1.0 O C:HOH303 2.2 65.9 1.0 OD1 C:ASP129 2.5 62.8 1.0 CG C:ASP129 2.6 61.3 1.0 OD1 C:ASP132 2.8 66.5 1.0 O C:HOH301 3.0 61.7 1.0 OD2 C:ASP132 3.1 67.9 1.0 CG C:ASP132 3.3 62.4 1.0 CB C:ASP129 4.1 57.7 1.0 CB C:ASP132 4.6 54.4 1.0 OD1 C:ASN128 4.9 64.2 1.0 N C:ASP129 4.9 63.3 1.0 N C:ASP132 5.0 50.1 1.0

Sodium binding site 4 out of 4 in the Avidin + Biotin-Tempo


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Avidin + Biotin-Tempo within 5.0Å range: probe atom residue distance (Å) B Occ D:Na203 b:61.4 occ:1.00 OD2 D:ASP129 2.2 63.5 1.0 O D:HOH301 2.3 58.5 1.0 OD2 D:ASP132 2.7 65.1 1.0 CG D:ASP129 2.9 67.3 1.0 OD1 D:ASP129 2.9 71.6 1.0 O D:HOH308 3.0 60.4 1.0 OD1 D:ASP132 3.2 65.9 1.0 CG D:ASP132 3.3 66.8 1.0 CB D:ASP129 4.4 61.0 1.0 CB D:ASP132 4.7 63.4 1.0

J.Milani, K.Lau, F.Pojer, J.P.Ansermet, F.Saenz. Avidin + Biotin-Tempo To Be Published.