Zinc 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:

Sodium

(Na)

4 atoms

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Avidin + Biotin-Tempo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:51.3 occ:1.00 OE2 A:GLU52 1.9 52.5 1.0 NE2 B:HIS74 2.3 35.7 1.0 O A:HOH315 2.3 30.3 1.0 O A:HOH313 2.6 44.9 1.0 CD A:GLU52 2.9 47.8 1.0 CD2 B:HIS74 3.1 44.4 1.0 CE1 B:HIS74 3.4 44.5 1.0 CG A:GLU52 3.4 49.9 1.0 NH1 A:ARG50 3.7 58.2 1.0 CB B:PRO72 3.8 43.2 1.0 CG B:PRO72 4.0 44.6 1.0 OE1 A:GLU52 4.1 53.8 1.0 CG B:HIS74 4.3 42.5 1.0 ND1 B:HIS74 4.4 41.6 1.0 CD A:ARG50 4.7 61.7 1.0 CB A:ARG50 4.8 47.9 1.0 CB A:GLU52 4.9 40.8 1.0 CZ A:ARG50 4.9 56.9 1.0 CG2 A:THR76 5.0 48.0 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Avidin + Biotin-Tempo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:55.3 occ:1.00 OE2 B:GLU52 2.0 54.9 1.0 NE2 A:HIS74 2.3 39.7 1.0 O A:HOH314 2.4 37.1 1.0 O B:HOH307 2.5 40.9 1.0 CD B:GLU52 2.9 49.0 1.0 CD2 A:HIS74 3.0 39.5 1.0 CG B:GLU52 3.3 42.9 1.0 CE1 A:HIS74 3.4 46.1 1.0 CB A:PRO72 3.9 37.0 1.0 NE B:ARG50 4.0 53.6 1.0 OE1 B:GLU52 4.1 51.7 1.0 CG A:PRO72 4.2 42.0 1.0 CG A:HIS74 4.2 41.2 1.0 CD B:ARG50 4.3 54.9 1.0 CB B:ARG50 4.4 48.9 1.0 ND1 A:HIS74 4.4 41.3 1.0 CG2 B:THR76 4.7 44.4 1.0 CB B:GLU52 4.8 36.4 1.0 CG B:ARG50 4.9 55.1 1.0 O B:ARG50 5.0 47.1 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Avidin + Biotin-Tempo within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:55.0 occ:1.00 OE2 C:GLU52 2.0 54.1 1.0 O D:HOH311 2.2 38.1 1.0 O C:HOH309 2.2 47.8 1.0 NE2 D:HIS74 2.3 40.4 1.0 CD C:GLU52 2.9 50.8 1.0 CD2 D:HIS74 3.1 43.9 1.0 CG C:GLU52 3.2 47.5 1.0 CE1 D:HIS74 3.4 48.0 1.0 NE C:ARG50 3.9 55.6 1.0 CB D:PRO72 3.9 42.9 1.0 CG D:PRO72 4.1 45.5 1.0 OE1 C:GLU52 4.1 51.0 1.0 CD C:ARG50 4.2 53.1 1.0 CG D:HIS74 4.3 42.3 1.0 CB C:ARG50 4.3 46.2 1.0 ND1 D:HIS74 4.4 47.7 1.0 CG2 C:THR76 4.6 49.8 1.0 CB C:GLU52 4.7 40.9 1.0 CG C:ARG50 4.9 46.7 1.0 CZ C:ARG50 4.9 56.3 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Avidin + Biotin-Tempo within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:52.3 occ:1.00 OE2 D:GLU52 2.0 53.8 1.0 O D:HOH310 2.3 31.4 1.0 NE2 C:HIS74 2.3 38.8 1.0 O D:HOH309 2.6 32.9 1.0 CD D:GLU52 2.8 49.0 1.0 CD2 C:HIS74 3.1 40.8 1.0 CG D:GLU52 3.1 47.1 1.0 CE1 C:HIS74 3.4 47.0 1.0 CB C:PRO72 3.8 37.1 1.0 OE1 D:GLU52 3.9 47.6 1.0 CG C:PRO72 4.0 40.3 1.0 CD D:ARG50 4.2 56.1 1.0 CG C:HIS74 4.3 41.4 1.0 NE D:ARG50 4.3 53.8 1.0 CB D:ARG50 4.3 46.0 1.0 ND1 C:HIS74 4.4 46.1 1.0 CB D:GLU52 4.6 36.7 1.0 CG D:ARG50 4.9 48.6 1.0

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