Zinc in PDB 8pi5: Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation

The structure of Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation, PDB code: 8pi5 was solved by E.Johansson, G.Schluckebier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.66 / 1.66
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	79.353, 79.353, 39.185, 90, 90, 120
R / Rfree (%)	15.4 / 17.9

The structure of Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation (pdb code 8pi5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation, PDB code: 8pi5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:17.8 occ:0.33 HE2 B:HIS10 1.3 22.4 1.0 O B:HOH235 1.9 24.8 0.3 NE2 B:HIS10 2.1 18.7 1.0 CD2 B:HIS10 2.9 18.4 1.0 HD2 B:HIS10 3.0 22.1 1.0 CE1 B:HIS10 3.2 25.9 1.0 HE1 B:HIS10 3.4 31.1 1.0 ZN B:ZN103 3.7 22.2 0.3 HD2 B:HIS5 4.0 31.7 1.0 CG B:HIS10 4.1 17.6 1.0 ND1 B:HIS10 4.2 22.6 1.0 CD2 B:HIS5 4.7 26.4 1.0 NE2 B:HIS5 4.8 22.7 1.0 O D:HOH226 4.9 30.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:26.9 occ:0.11 O D:HOH226 2.0 30.0 1.0 O D:HOH205 2.0 24.2 1.0 O D:HOH242 3.3 22.4 0.3 OE2 D:GLU13 3.9 36.4 1.0 OE1 D:GLU13 4.0 32.1 1.0 OE2 B:GLU13 4.0 37.7 1.0 HE1 B:HIS10 4.0 31.1 1.0 OE1 B:GLU13 4.3 42.8 1.0 CD D:GLU13 4.3 34.7 1.0 CD B:GLU13 4.6 34.3 1.0 O B:HOH205 4.6 39.6 1.0 CE1 B:HIS10 4.6 25.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:22.2 occ:0.33 O B:HOH235 1.9 24.8 0.3 NE2 B:HIS5 2.1 22.7 1.0 CE1 B:HIS5 3.1 23.4 1.0 CD2 B:HIS5 3.1 26.4 1.0 HD2 B:HIS5 3.2 31.7 1.0 HE1 B:HIS5 3.2 28.1 1.0 HB2 B:CYS7 3.6 22.8 1.0 ZN B:ZN101 3.7 17.8 0.3 ND1 B:HIS5 4.2 24.6 1.0 CG B:HIS5 4.2 25.3 1.0 CB B:CYS7 4.4 19.0 1.0 HD2 B:HIS10 4.5 22.1 1.0 HE2 B:HIS10 4.5 22.4 1.0 O B:HOH242 4.5 24.4 0.3 HB3 B:CYS7 4.6 22.8 1.0 SG B:CYS7 4.8 21.4 1.0 HD1 B:HIS5 4.9 29.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Insulin DESB30 Precursor with An Alanine- Methionine-Lysine C-Peptide in Hexamer (T3R3) Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:18.5 occ:0.33 CL D:CL102 2.0 22.4 0.3 NE2 D:HIS10 2.1 16.7 1.0 CD2 D:HIS10 3.0 18.4 1.0 CE1 D:HIS10 3.1 21.7 1.0 HD2 D:HIS10 3.2 22.1 1.0 HE1 D:HIS10 3.3 26.0 1.0 HB3 D:LEU6 3.8 22.7 1.0 HD13 D:LEU6 4.2 29.5 1.0 CG D:HIS10 4.2 16.1 1.0 ND1 D:HIS10 4.2 19.9 1.0 CB D:LEU6 4.8 18.9 1.0 O D:LEU6 4.8 18.4 1.0 HD22 D:LEU6 4.9 27.4 1.0 HD1 D:HIS10 5.0 23.9 1.0

T.Kjeldsen, A.S.Andersen, F.Hubalek, E.Johansson, F.F.Kreiner, G.Schluckebier, P.Kurtzhals. Molecular Engineering of Insulin For Recombinant Expression in Yeast. Trends Biotechnol 2023.
ISSN: ISSN 1879-3096
PubMed: 37880066
DOI: 10.1016/J.TIBTECH.2023.09.012