Zinc in PDB 8ein: Crystal Structure of Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587

The structure of Crystal Structure of Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587, PDB code: 8ein was solved by I.Sharon, T.M.Schmeing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.94 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	152.632, 128.015, 107.078, 90, 129.48, 90
R / Rfree (%)	24.2 / 26.2

The structure of Crystal Structure of Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587 also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587 (pdb code 8ein). 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 Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587, PDB code: 8ein:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587


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 Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:101.3 occ:1.00 ND1 A:HIS179 2.3 73.7 1.0 OE1 A:GLU53 2.4 81.8 1.0 ND1 A:HIS50 2.6 60.8 1.0 OE2 A:GLU53 2.7 76.9 1.0 CD A:GLU53 2.9 69.5 1.0 OE2 A:GLU251 3.2 87.4 1.0 CG A:HIS179 3.2 73.9 1.0 CE1 A:HIS179 3.3 75.5 1.0 CE1 A:HIS50 3.3 69.7 1.0 CB A:HIS179 3.4 62.8 1.0 O A:ALA180 3.5 66.2 1.0 CG A:HIS50 3.7 62.7 1.0 NH1 A:ARG102 4.0 105.5 1.0 CB A:HIS50 4.2 66.3 1.0 N A:ALA180 4.3 73.2 1.0 CD2 A:HIS179 4.3 78.7 1.0 NE2 A:HIS179 4.4 77.5 1.0 CD A:GLU251 4.4 89.7 1.0 CA A:HIS179 4.4 68.5 1.0 CG A:GLU53 4.4 64.2 1.0 NE2 A:HIS50 4.6 63.2 1.0 C A:ALA180 4.7 64.9 1.0 CD2 A:HIS50 4.8 56.9 1.0 C A:HIS179 4.9 68.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587


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 Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:72.9 occ:1.00 ND1 B:HIS179 2.4 77.8 1.0 ND1 B:HIS50 2.4 69.0 1.0 OE2 B:GLU53 2.7 92.8 1.0 OE1 B:GLU53 2.7 83.8 1.0 CE1 B:HIS50 3.0 68.7 1.0 CD B:GLU53 3.0 64.3 1.0 CE1 B:HIS179 3.3 84.9 1.0 CG B:HIS179 3.4 74.6 1.0 OE2 B:GLU251 3.5 82.5 1.0 CG B:HIS50 3.6 63.0 1.0 CB B:HIS179 3.7 67.5 1.0 O B:ALA180 3.8 69.4 1.0 NH1 B:ARG102 3.9 74.3 1.0 CB B:HIS50 4.1 61.9 1.0 NE2 B:HIS50 4.3 66.5 1.0 NE2 B:HIS179 4.4 87.2 1.0 CD2 B:HIS179 4.4 78.7 1.0 CG B:GLU53 4.6 55.6 1.0 CD2 B:HIS50 4.6 69.5 1.0 CD B:GLU251 4.6 66.9 1.0 N B:ALA180 4.6 68.0 1.0 CA B:HIS179 4.7 73.3 1.0 NH2 B:ARG102 4.8 91.1 1.0 CZ B:ARG102 4.8 88.6 1.0 C B:ALA180 5.0 63.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587


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 Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:91.7 occ:1.00 ND1 C:HIS50 2.4 75.0 1.0 ND1 C:HIS179 2.4 85.5 1.0 OE1 C:GLU53 2.4 74.5 1.0 OE2 C:GLU53 2.6 91.0 1.0 CD C:GLU53 2.8 71.9 1.0 CE1 C:HIS50 3.2 80.5 1.0 CG C:HIS179 3.3 75.4 1.0 CE1 C:HIS179 3.3 66.0 1.0 CB C:HIS179 3.5 72.1 1.0 CG C:HIS50 3.6 74.8 1.0 O C:ALA180 3.6 80.7 1.0 NH1 C:ARG102 3.9 112.2 1.0 OE2 C:GLU251 4.0 105.6 1.0 CB C:HIS50 4.0 66.4 1.0 CG C:GLU53 4.3 58.2 1.0 NE2 C:HIS50 4.4 62.9 1.0 N C:ALA180 4.4 57.5 1.0 CD2 C:HIS179 4.4 70.0 1.0 NE2 C:HIS179 4.4 78.6 1.0 CA C:HIS179 4.5 59.5 1.0 CD2 C:HIS50 4.6 77.0 1.0 CD C:GLU251 4.8 99.9 1.0 C C:ALA180 4.8 67.6 1.0 CZ C:ARG102 4.9 102.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587


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 Wt Cyanophycin Dipeptide Hydrolase Cphz From Acinetobacter Baylyi DSM587 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:88.2 occ:1.00 ND1 D:HIS50 2.2 79.6 1.0 ND1 D:HIS179 2.4 68.4 1.0 OE1 D:GLU53 2.5 70.1 1.0 OE2 D:GLU53 2.5 84.6 1.0 CD D:GLU53 2.8 70.5 1.0 CE1 D:HIS50 3.0 81.6 1.0 CE1 D:HIS179 3.2 74.6 1.0 CG D:HIS50 3.3 70.4 1.0 CG D:HIS179 3.4 65.5 1.0 CB D:HIS179 3.8 71.0 1.0 CB D:HIS50 3.8 66.1 1.0 O D:ALA180 3.8 62.5 1.0 OE2 D:GLU251 3.8 88.7 1.0 NH1 D:ARG102 3.8 90.7 1.0 NE2 D:HIS50 4.2 70.6 1.0 CG D:GLU53 4.3 59.6 1.0 CD2 D:HIS50 4.4 73.6 1.0 NE2 D:HIS179 4.4 86.7 1.0 CD2 D:HIS179 4.5 68.3 1.0 N D:ALA180 4.6 74.5 1.0 CA D:HIS179 4.7 63.4 1.0 CZ D:ARG102 4.8 93.4 1.0 CD D:GLU251 4.9 78.9 1.0 NH2 D:ARG102 5.0 89.3 1.0 C D:ALA180 5.0 68.1 1.0

I.Sharon, G.A.Mckay, D.Nguyen, T.M.Schmeing. Discovery of Cyanophycin Dipeptide Hydrolase Enzymes Suggests Widespread Utility of the Natural Biopolymer Cyanophycin. Proc.Natl.Acad.Sci.Usa V. 120 47120 2023.
ISSN: ESSN 1091-6490
PubMed: 36800389
DOI: 10.1073/PNAS.2216547120