Zinc in PDB 6yra: Crystal Structure of Atp-Dependent Caprolactamase From Pseudomonas Jessenii

The structure of Crystal Structure of Atp-Dependent Caprolactamase From Pseudomonas Jessenii, PDB code: 6yra was solved by H.J.Rozeboom, D.B.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.84 / 4.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	195.377, 167.367, 87.965, 90, 90, 90
R / Rfree (%)	23.9 / 38.1

The binding sites of Zinc atom in the Crystal Structure of Atp-Dependent Caprolactamase From Pseudomonas Jessenii (pdb code 6yra). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Atp-Dependent Caprolactamase From Pseudomonas Jessenii, PDB code: 6yra:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Atp-Dependent Caprolactamase From Pseudomonas Jessenii


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 Atp-Dependent Caprolactamase From Pseudomonas Jessenii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn600 b:48.5 occ:1.00 OD2 B:ASP41 1.8 86.7 1.0 OD2 B:ASP102 1.9 80.8 1.0 OD1 B:ASP102 2.0 78.9 1.0 NE2 B:HIS99 2.0 57.3 1.0 OD1 B:ASP41 2.1 71.5 1.0 ND1 B:HIS124 2.2 99.8 1.0 CG B:ASP102 2.2 74.1 1.0 CG B:ASP41 2.3 72.5 1.0 CE1 B:HIS124 2.5 81.2 1.0 CE1 B:HIS99 2.9 49.5 1.0 CD2 B:HIS99 3.0 47.8 1.0 CG B:HIS124 3.5 94.0 1.0 CB B:ASP41 3.7 72.9 1.0 CB B:ASP102 3.7 49.0 1.0 NE2 B:HIS124 3.8 92.7 1.0 ND1 B:HIS99 4.0 50.5 1.0 CG B:HIS99 4.0 46.5 1.0 CD2 B:LEU38 4.1 96.5 1.0 CD2 B:HIS124 4.3 92.9 1.0 CB B:HIS124 4.4 78.3 1.0 O B:ASP41 4.4 76.1 1.0 CA B:ASP102 4.6 31.3 1.0 N B:ASP102 4.6 28.1 1.0 CA B:ASP41 4.7 68.6 1.0 C B:ASP41 5.0 71.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Atp-Dependent Caprolactamase From Pseudomonas Jessenii


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 Atp-Dependent Caprolactamase From Pseudomonas Jessenii within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn600 b:52.1 occ:1.00 OD2 D:ASP102 2.0 37.2 1.0 OD2 D:ASP41 2.0 98.7 1.0 OD1 D:ASP102 2.0 31.2 1.0 ND1 D:HIS124 2.1 94.7 1.0 NE2 D:HIS99 2.2 70.0 1.0 OD1 D:ASP41 2.2 105.2 1.0 CG D:ASP102 2.3 27.4 1.0 CE1 D:HIS99 2.3 66.2 1.0 CG D:ASP41 2.4 99.5 1.0 CE1 D:HIS124 2.9 90.1 1.0 CG D:HIS124 3.3 88.0 1.0 CD2 D:HIS99 3.5 65.2 1.0 ND1 D:HIS99 3.6 64.5 1.0 CB D:HIS124 3.8 82.8 1.0 CB D:ASP102 3.8 24.5 1.0 CB D:ASP41 4.0 82.7 1.0 NE2 D:HIS124 4.1 88.3 1.0 CG D:HIS99 4.2 64.3 1.0 CD2 D:HIS124 4.3 88.3 1.0 CA D:HIS124 4.4 76.4 1.0 O D:ASP41 4.5 57.2 1.0 CA D:ASP102 4.6 23.7 1.0 N D:HIS124 4.8 62.7 1.0 N D:ASP102 4.8 23.6 1.0 CD2 D:LEU38 4.8 36.3 1.0 CA D:ASP41 4.9 62.5 1.0 NE2 D:HIS63 4.9 24.4 1.0

A.Marjanovic, H.J.Rozeboom, M.S.De Vries, C.Mayer, M.Otzen, H.J.Wijma, D.B.Janssen. Catalytic and Structural Properties of Atp-Dependent Caprolactamase From Pseudomonas Jessenii. Proteins 2021.
ISSN: ESSN 1097-0134
PubMed: 33826169
DOI: 10.1002/PROT.26082