Zinc in PDB 5yxc: Crystal Structure of Zinc Binding Protein Zint in Complex with Citrate From E. Coli

The structure of Crystal Structure of Zinc Binding Protein Zint in Complex with Citrate From E. Coli, PDB code: 5yxc was solved by J.Chen, L.Wang, F.Shang, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.03 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.040, 65.866, 73.536, 90.00, 91.35, 90.00
R / Rfree (%)	18.8 / 23.4

The binding sites of Zinc atom in the Crystal Structure of Zinc Binding Protein Zint in Complex with Citrate From E. Coli (pdb code 5yxc). 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 Zinc Binding Protein Zint in Complex with Citrate From E. Coli, PDB code: 5yxc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Zinc Binding Protein Zint in Complex with Citrate From E. Coli


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 Zinc Binding Protein Zint in Complex with Citrate From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.1 occ:1.00 HO7 A:CIT302 1.4 17.7 1.0 NE2 A:HIS167 2.1 12.8 1.0 O7 A:CIT302 2.1 14.8 1.0 NE2 A:HIS178 2.1 10.9 1.0 O6 A:CIT302 2.1 12.7 1.0 O2 A:CIT302 2.1 15.5 1.0 NE2 A:HIS176 2.2 13.2 1.0 C6 A:CIT302 2.8 21.6 1.0 C3 A:CIT302 2.9 16.8 1.0 CE1 A:HIS178 3.0 13.6 1.0 CE1 A:HIS167 3.0 17.6 1.0 CD2 A:HIS167 3.0 14.0 1.0 HE1 A:HIS178 3.1 16.3 1.0 C1 A:CIT302 3.1 21.3 1.0 CE1 A:HIS176 3.1 11.7 1.0 HE1 A:HIS167 3.2 21.1 1.0 CD2 A:HIS178 3.2 13.3 1.0 CD2 A:HIS176 3.2 10.4 1.0 HD2 A:HIS167 3.2 16.8 1.0 HE1 A:HIS176 3.3 14.1 1.0 HD2 A:HIS176 3.4 12.5 1.0 HD2 A:HIS178 3.5 15.9 1.0 C2 A:CIT302 3.5 18.2 1.0 O5 A:CIT302 4.0 17.4 1.0 H22 A:CIT302 4.0 21.9 1.0 O4 A:CIT302 4.0 17.0 1.0 ND1 A:HIS167 4.1 15.9 1.0 ND1 A:HIS178 4.1 11.4 1.0 CG A:HIS167 4.2 12.6 1.0 O1 A:CIT302 4.2 22.5 1.0 C4 A:CIT302 4.2 18.6 1.0 ND1 A:HIS176 4.3 13.8 1.0 CG A:HIS178 4.3 11.2 1.0 O A:HOH461 4.3 35.0 1.0 CG A:HIS176 4.3 13.4 1.0 O A:HOH560 4.4 27.7 1.0 H21 A:CIT302 4.4 21.9 1.0 C5 A:CIT302 4.5 22.3 1.0 HG23 A:THR198 4.7 14.2 1.0 H41 A:CIT302 4.8 22.3 1.0 H42 A:CIT302 5.0 22.3 1.0 HG21 A:THR198 5.0 14.2 1.0 HA A:ASP166 5.0 10.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Zinc Binding Protein Zint in Complex with Citrate From E. Coli


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 Zinc Binding Protein Zint in Complex with Citrate From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:14.8 occ:0.96 HO7 B:CIT302 1.4 19.6 1.0 NE2 B:HIS167 2.0 14.5 1.0 O6 B:CIT302 2.1 17.1 1.0 NE2 B:HIS178 2.1 12.0 1.0 O2 B:CIT302 2.1 16.5 1.0 O7 B:CIT302 2.2 16.4 1.0 NE2 B:HIS176 2.2 14.2 1.0 C6 B:CIT302 2.8 23.8 1.0 C3 B:CIT302 2.9 16.9 1.0 CE1 B:HIS167 3.0 18.7 1.0 CD2 B:HIS167 3.0 13.9 1.0 CE1 B:HIS178 3.0 17.7 1.0 C1 B:CIT302 3.1 23.3 1.0 CD2 B:HIS178 3.1 15.5 1.0 CE1 B:HIS176 3.2 15.4 1.0 HE1 B:HIS167 3.2 22.5 1.0 HE1 B:HIS178 3.2 21.2 1.0 HD2 B:HIS167 3.2 16.7 1.0 CD2 B:HIS176 3.2 13.7 1.0 HD2 B:HIS178 3.3 18.6 1.0 HE1 B:HIS176 3.3 18.5 1.0 HD2 B:HIS176 3.4 16.4 1.0 C2 B:CIT302 3.5 17.9 1.0 O5 B:CIT302 4.0 21.7 1.0 H22 B:CIT302 4.0 21.5 1.0 O4 B:CIT302 4.1 22.0 1.0 ND1 B:HIS167 4.1 19.9 1.0 CG B:HIS167 4.2 14.3 1.0 ND1 B:HIS178 4.2 12.9 1.0 O1 B:CIT302 4.2 23.5 1.0 CG B:HIS178 4.3 12.4 1.0 C4 B:CIT302 4.3 21.5 1.0 ND1 B:HIS176 4.3 16.5 1.0 O B:HOH536 4.3 25.7 1.0 CG B:HIS176 4.4 17.3 1.0 H21 B:CIT302 4.4 21.5 1.0 O B:HOH528 4.4 46.2 1.0 C5 B:CIT302 4.6 25.1 1.0 HG23 B:THR198 4.8 16.3 1.0 H42 B:CIT302 4.8 25.8 1.0 HA B:ASP166 4.9 15.7 1.0 H41 B:CIT302 5.0 25.8 1.0

J.Chen, L.Wang, F.Shang, Y.Dong, N.C.Ha, K.H.Nam, C.Quan, Y.Xu. Crystal Structure of E. Coli Zint with One Zinc-Binding Mode and Complexed with Citrate Biochem. Biophys. Res. V. 500 139 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 29596824
DOI: 10.1016/J.BBRC.2018.03.192