Zinc in PDB 3erp: Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium

The structure of Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium, PDB code: 3erp was solved by A.U.Singer, G.Minasov, E.Evdokimova, J.S.Brunzelle, M.Kudritska, A.M.Edwards, W.F.Anderson, A.Savchenko, Center For Structural Genomicsof Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.96 / 1.55
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	127.096, 127.096, 120.492, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.8

The structure of Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium also contains other interesting chemical elements:

Arsenic	(As)	2 atoms
Chlorine	(Cl)	5 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium (pdb code 3erp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium, PDB code: 3erp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn333 b:24.7 occ:0.40 NE2 A:HIS155 2.1 21.4 1.0 O A:HOH765 2.1 26.6 1.0 O A:HOH767 2.3 19.8 0.7 O A:HOH770 2.5 38.2 0.7 CE1 A:HIS155 3.0 19.4 1.0 CD2 A:HIS155 3.1 19.3 1.0 O A:HOH766 3.2 41.6 1.0 ND1 A:HIS159 3.6 28.0 0.3 CE1 A:HIS159 3.6 24.2 0.3 O A:HOH767 3.6 16.9 0.3 NE2 A:HIS159 3.9 25.1 0.3 CG A:HIS159 3.9 22.2 0.3 CD2 A:HIS159 4.0 19.4 0.3 ND1 A:HIS155 4.1 18.6 1.0 CG A:HIS155 4.2 16.6 1.0 CB A:HIS159 4.6 20.1 0.3 CD1 A:ILE117 4.7 19.2 1.0 CB A:HIS159 4.7 23.1 0.7 O A:HOH631 4.7 28.8 1.0 NZ A:LYS161 4.8 20.7 0.3 CG A:HIS159 4.8 26.1 0.7 NZ A:LYS161 4.9 20.9 0.7 CG2 A:ILE117 4.9 15.9 1.0 CD2 A:HIS159 5.0 25.8 0.7

Zinc binding site 2 out of 2 in the Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn333 b:19.9 occ:0.30 NE2 B:HIS155 2.0 20.6 1.0 O B:HOH897 2.1 23.0 0.7 O B:HOH895 2.2 29.2 1.0 O B:HOH901 2.5 37.4 0.5 CD2 B:HIS155 3.0 18.0 1.0 CE1 B:HIS155 3.0 20.2 1.0 O B:HOH896 3.3 36.9 1.0 O B:HOH897 3.3 16.7 0.3 CD2 B:HIS159 3.9 25.8 0.3 CG B:HIS159 4.0 22.0 0.3 NE2 B:HIS159 4.0 24.6 0.3 ND1 B:HIS155 4.1 19.7 1.0 CG B:HIS155 4.1 18.0 1.0 ND1 B:HIS159 4.1 19.3 0.3 CE1 B:HIS159 4.2 26.1 0.3 NZ B:LYS161 4.5 21.9 0.7 CB B:HIS159 4.6 18.2 0.3 O B:HOH814 4.7 28.7 1.0 CB B:HIS159 4.7 21.2 0.7 CD1 B:ILE117 4.7 18.1 1.0 CG B:HIS159 4.8 23.7 0.7 CG2 B:ILE117 4.8 14.7 1.0 CD2 B:HIS159 4.8 26.5 0.7

T.Kim, R.Flick, J.Brunzelle, A.Singer, E.Evdokimova, G.Brown, J.C.Joo, G.A.Minasov, W.F.Anderson, R.Mahadevan, A.Savchenko, A.F.Yakunin. Structural and Biochemical Studies of Novel Aldo-Keto Reductases For the Biocatalytic Conversion of 3-Hydroxybutanal to 1,3-Butanediol. Appl.Environ.Microbiol. 2017.
ISSN: ESSN 1098-5336
PubMed: 28130301
DOI: 10.1128/AEM.03172-16