Zinc in PDB 8xjg: Crystal Structure of the Yqey Protein From Vibrio Parahaemolyticus

The structure of Crystal Structure of the Yqey Protein From Vibrio Parahaemolyticus, PDB code: 8xjg was solved by S.Y.Kim, S.I.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.14 / 1.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.721, 107.577, 34.671, 90, 90, 90
R / Rfree (%)	22.7 / 25.8

The binding sites of Zinc atom in the Crystal Structure of the Yqey Protein From Vibrio Parahaemolyticus (pdb code 8xjg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Yqey Protein From Vibrio Parahaemolyticus, PDB code: 8xjg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Yqey Protein From Vibrio Parahaemolyticus


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 Yqey Protein From Vibrio Parahaemolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:19.9 occ:0.79 OE1 A:GLU79 1.8 22.3 1.0 O A:HOH330 2.0 25.7 1.0 OE1 A:GLU82 2.1 20.0 1.0 OE2 A:GLU82 2.4 18.0 1.0 CD A:GLU82 2.5 19.1 1.0 CD A:GLU79 2.6 25.3 1.0 OE2 A:GLU79 2.8 27.8 1.0 O A:HOH301 3.5 39.1 1.0 CG A:GLU79 4.0 27.5 1.0 CG A:GLU82 4.0 16.1 1.0 O A:HOH374 4.1 29.3 1.0 O A:HOH343 4.2 23.0 1.0 O A:HOH327 4.5 24.1 1.0 CA A:GLU79 4.5 22.3 1.0 CG1 A:VAL78 4.6 19.5 1.0 CB A:GLU79 4.7 22.0 1.0 NE A:ARG60 4.7 24.9 1.0 CG A:ARG60 4.8 22.3 1.0 CB A:GLU82 4.8 17.2 1.0 N A:GLU79 4.9 22.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Yqey Protein From Vibrio Parahaemolyticus


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 Yqey Protein From Vibrio Parahaemolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:20.7 occ:0.81 O A:HOH328 2.1 26.3 1.0 O A:HOH348 2.1 28.2 1.0 O A:HOH378 4.2 30.8 1.0 OE1 A:GLN6 4.2 22.2 1.0 O A:PHE89 4.3 29.7 1.0 O A:GLU88 4.3 25.9 1.0 NE2 A:GLN6 4.4 20.9 1.0 C A:PHE89 4.6 29.9 1.0 O A:MET90 4.7 39.2 1.0 CD A:GLN6 4.8 19.7 1.0 CA A:PHE89 4.8 26.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Yqey Protein From Vibrio Parahaemolyticus


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 the Yqey Protein From Vibrio Parahaemolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:40.1 occ:0.46 OE2 A:GLU10 2.2 48.8 1.0 OE1 A:GLU88 2.4 53.1 1.0 CD A:GLU10 2.8 35.9 1.0 OE1 A:GLU10 2.8 39.0 1.0 OE2 A:GLU88 3.1 51.0 1.0 CD A:GLU88 3.1 49.6 1.0 NH2 A:ARG22 3.8 46.4 1.0 CG A:GLU10 4.2 32.3 1.0 NE A:ARG22 4.3 35.9 1.0 CZ A:ARG22 4.3 37.7 1.0 CG A:GLU88 4.6 39.5 1.0

S.Y.Kim, S.I.Yoon. Structural Analysis of the Yqey Proteins From Campylobacter Jejuni and Vibrio Parahaemolyticus. Biochem.Biophys.Res.Commun. V. 695 49485 2024.
ISSN: ESSN 1090-2104
PubMed: 38211535
DOI: 10.1016/J.BBRC.2024.149485