Zinc in PDB 4cob: Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa

All present enzymatic activity of Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa:
3.5.1.9;

The structure of Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa, PDB code: 4cob was solved by L.Diaz-Saez, V.Srikannathasan, M.Zoltner, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.62 / 2.37
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.721, 112.721, 90.761, 90.00, 90.00, 120.00
R / Rfree (%)	15.047 / 19.367

The binding sites of Zinc atom in the Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa (pdb code 4cob). 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 Kynurenine Formamidase From Pseudomonas Aeruginosa, PDB code: 4cob:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:54.2 occ:1.00 OD2 A:ASP56 2.0 38.9 1.0 OE2 A:GLU173 2.2 35.6 1.0 NE2 A:HIS161 2.2 37.0 1.0 O A:HOH2042 2.4 40.2 1.0 OE1 A:GLU173 2.5 34.9 1.0 CD A:GLU173 2.7 36.8 1.0 ZN A:ZN402 3.0 47.3 1.0 CG A:ASP56 3.0 33.1 1.0 CE1 A:HIS161 3.1 34.6 1.0 CD2 A:HIS161 3.3 36.2 1.0 OD1 A:ASP56 3.3 36.5 1.0 O A:HOH2041 3.5 38.6 1.0 O A:HOH2034 3.8 38.1 1.0 CD2 A:HIS60 4.0 37.9 1.0 NE2 A:HIS60 4.1 38.3 1.0 CG A:GLU173 4.2 35.4 1.0 ND1 A:HIS161 4.2 34.7 1.0 CB A:ASP56 4.3 37.7 1.0 OG A:SER149 4.3 36.1 1.0 CG A:HIS161 4.4 32.3 1.0 O A:HOH2037 4.4 56.2 1.0 O A:PRO148 4.7 41.6 1.0 CG2 A:ILE171 4.7 38.4 1.0 NE2 A:HIS54 4.8 36.2 1.0 CA A:SER149 4.8 33.5 1.0 ND1 A:HIS50 4.8 36.5 1.0 N A:LEU150 4.9 35.6 1.0 CB A:SER149 4.9 37.9 1.0 CE1 A:HIS50 5.0 36.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:47.3 occ:1.00 NE2 A:HIS54 2.2 36.2 1.0 OD1 A:ASP56 2.2 36.5 1.0 OE1 A:GLU173 2.3 34.9 1.0 ND1 A:HIS50 2.3 36.5 1.0 O A:HOH2034 2.4 38.1 1.0 O A:HOH2042 2.6 40.2 1.0 ZN A:ZN401 3.0 54.2 1.0 CE1 A:HIS50 3.1 36.9 1.0 CD2 A:HIS54 3.1 35.0 1.0 CE1 A:HIS54 3.1 38.3 1.0 CG A:ASP56 3.1 33.1 1.0 OD2 A:ASP56 3.4 38.9 1.0 CG A:HIS50 3.4 39.6 1.0 CD A:GLU173 3.5 36.8 1.0 O A:HOH2037 3.9 56.2 1.0 CB A:HIS50 3.9 38.4 1.0 OE2 A:GLU173 4.1 35.6 1.0 ND1 A:HIS54 4.2 38.6 1.0 NE2 A:HIS50 4.3 35.3 1.0 CG A:HIS54 4.3 34.7 1.0 NE2 A:HIS60 4.4 38.3 1.0 O A:PRO148 4.4 41.6 1.0 CD2 A:HIS50 4.5 34.2 1.0 O A:HOH2041 4.5 38.6 1.0 CB A:ASP56 4.5 37.7 1.0 CD2 A:HIS60 4.6 37.9 1.0 CA A:HIS50 4.7 38.8 1.0 CG A:GLU173 4.7 35.4 1.0 CB A:GLU173 4.8 33.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:74.5 occ:1.00 OD2 B:ASP56 2.1 56.9 1.0 OE2 B:GLU173 2.3 52.7 1.0 NE2 B:HIS161 2.4 63.1 1.0 O B:HOH2028 2.5 48.5 1.0 OE1 B:GLU173 2.8 46.6 1.0 CD B:GLU173 2.9 47.4 1.0 ZN B:ZN402 2.9 53.9 1.0 CG B:ASP56 3.1 52.2 1.0 CE1 B:HIS161 3.3 54.7 1.0 OD1 B:ASP56 3.3 41.5 1.0 O B:HOH2023 3.4 43.3 1.0 CD2 B:HIS161 3.4 59.9 1.0 NE2 B:HIS60 3.8 58.8 1.0 CD2 B:HIS60 3.9 56.1 1.0 CG B:GLU173 4.4 41.4 1.0 OG B:SER149 4.4 52.3 1.0 ND1 B:HIS161 4.4 62.4 1.0 CB B:ASP56 4.5 50.2 1.0 CG B:HIS161 4.5 62.2 1.0 O B:PRO148 4.6 51.5 1.0 ND1 B:HIS50 4.6 45.3 1.0 CE1 B:HIS50 4.7 41.3 1.0 NE2 B:HIS54 4.8 45.0 1.0 O B:HOH2026 4.8 56.9 1.0 CA B:SER149 4.8 46.0 1.0 CB B:SER149 4.8 47.2 1.0 CG2 B:ILE171 4.8 44.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Kynurenine Formamidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:53.9 occ:1.00 NE2 B:HIS54 2.2 45.0 1.0 O B:HOH2023 2.2 43.3 1.0 OE1 B:GLU173 2.2 46.6 1.0 OD1 B:ASP56 2.2 41.5 1.0 ND1 B:HIS50 2.2 45.3 1.0 ZN B:ZN401 2.9 74.5 1.0 CE1 B:HIS50 2.9 41.3 1.0 CD2 B:HIS54 2.9 39.7 1.0 CG B:ASP56 3.2 52.2 1.0 CE1 B:HIS54 3.3 43.1 1.0 O B:HOH2028 3.4 48.5 1.0 OD2 B:ASP56 3.4 56.9 1.0 CD B:GLU173 3.4 47.4 1.0 CG B:HIS50 3.5 47.9 1.0 OE2 B:GLU173 3.9 52.7 1.0 CB B:HIS50 4.0 50.3 1.0 CG B:HIS54 4.1 38.7 1.0 NE2 B:HIS50 4.1 44.8 1.0 ND1 B:HIS54 4.3 45.0 1.0 O B:HOH2026 4.3 56.9 1.0 NE2 B:HIS60 4.4 58.8 1.0 CD2 B:HIS50 4.4 42.9 1.0 O B:PRO148 4.4 51.5 1.0 CB B:ASP56 4.6 50.2 1.0 CA B:HIS50 4.6 51.5 1.0 CG B:GLU173 4.7 41.4 1.0 CD2 B:HIS60 4.7 56.1 1.0 CB B:GLU173 4.9 38.7 1.0 CE1 B:HIS60 5.0 49.1 1.0

L.Diaz-Saez, V.Srikannathasan, M.Zoltner, W.N.Hunter. Structure of Bacterial Kynurenine Formamidase Reveals A Crowded Binuclear-Zinc Catalytic Site Primed to Generate A Potent Nucleophile. Biochem.J. V. 462 581 2014.
ISSN: ISSN 0264-6021
PubMed: 24942958
DOI: 10.1042/BJ20140511