Zinc in PDB 5xzi: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB5, PDB code: 5xzi was solved by W.J.Song, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.67 / 2.65
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	50.290, 98.000, 99.330, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 26.3

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB5 also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB5 (pdb code 5xzi). 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 the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB5, PDB code: 5xzi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB5


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 the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:37.9 occ:1.00 ND1 A:HIS63 2.0 34.0 1.0 CL A:CL204 2.3 34.0 1.0 CE1 A:HIS63 2.9 30.9 1.0 CG A:HIS63 3.1 35.0 1.0 CB A:HIS63 3.5 37.7 1.0 CA A:HIS63 3.9 38.6 1.0 CB A:TRP66 3.9 31.4 1.0 CG A:TRP66 4.0 30.9 1.0 NE2 A:HIS63 4.1 34.0 1.0 CD2 A:HIS63 4.2 32.8 1.0 CD1 A:TRP66 4.4 30.2 1.0 CD2 A:TRP66 4.6 32.2 1.0 N A:HIS63 4.7 41.7 1.0 O A:HOH344 4.9 35.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB5


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 the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:52.9 occ:1.00 O A:HOH345 2.1 16.5 1.0 ND1 A:HIS100 2.1 58.4 1.0 CE1 A:HIS100 2.8 56.5 1.0 CG A:HIS100 3.3 54.4 1.0 CB A:HIS100 3.9 50.4 1.0 NE2 A:HIS100 4.0 56.1 1.0 CA A:HIS100 4.2 48.8 1.0 CD2 A:HIS100 4.3 57.6 1.0 O A:HIS100 4.5 44.4 1.0 O A:HOH347 4.5 44.1 1.0 CD A:LYS104 4.7 67.7 1.0 O A:HOH341 4.8 40.4 1.0 C A:HIS100 4.8 48.1 1.0 NZ A:LYS104 4.8 79.3 1.0 CE A:LYS104 5.0 75.6 1.0

W.J.Song, J.Yu, F.A.Tezcan. Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-Beta-Lactamases. J. Am. Chem. Soc. V. 139 16772 2017.
ISSN: ESSN 1520-5126
PubMed: 28992705
DOI: 10.1021/JACS.7B08981