Arsenic 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:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	5 atoms
Sodium	(Na)	2 atoms

The binding sites of Arsenic 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 Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Structure of IDP01002, A Putative Oxidoreductase From and Essential Gene of Salmonella Typhimurium, PDB code: 3erp:
Jump to Arsenic binding site number: 1; 2;

Arsenic 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 Arsenic with other atoms in the As 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:As337 b:30.2 occ:0.60 AS A:CAC337 0.0 30.2 0.6 O2 A:CAC337 1.8 18.6 0.6 O1 A:CAC337 1.8 17.7 0.6 C1 A:CAC337 2.0 25.8 0.6 C2 A:CAC337 2.0 24.2 0.6 NA A:NA334 3.4 35.0 1.0 CZ A:PHE221 3.5 17.6 0.3 CE1 A:PHE221 3.6 16.7 0.3 NE2 A:HIS138 3.7 14.8 1.0 CE2 A:PHE221 4.0 17.5 0.3 OH A:TYR66 4.1 20.4 1.0 O A:HOH771 4.2 30.4 0.6 CD1 A:PHE221 4.2 18.0 0.3 CE2 A:TRP33 4.3 25.0 0.7 CZ2 A:TRP33 4.3 29.4 0.7 CZ A:PHE221 4.4 15.4 0.7 C1 A:EDO342 4.4 28.4 1.0 CE1 A:PHE221 4.4 15.8 0.7 CD2 A:HIS138 4.5 15.3 1.0 CD2 A:TRP33 4.6 23.7 0.7 CH2 A:TRP33 4.6 29.6 0.7 CD2 A:PHE221 4.6 14.3 0.3 CE1 A:HIS138 4.6 16.9 1.0 NE1 A:TRP33 4.6 21.1 0.7 CG A:PHE221 4.7 15.7 0.3 CD1 A:PHE221 4.8 16.3 0.7 ND2 A:ASN169 4.8 18.4 1.0 CE2 A:PHE221 4.8 16.6 0.7 CZ3 A:TRP33 4.9 29.1 0.7 CE3 A:TRP33 4.9 29.6 0.7 CE1 A:TYR66 4.9 16.6 1.0 O1 A:EDO342 4.9 28.6 1.0 CZ A:TYR66 5.0 19.7 1.0

Arsenic 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 Arsenic with other atoms in the As 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:As338 b:27.5 occ:0.70 AS B:CAC338 0.0 27.5 0.7 O2 B:CAC338 1.7 16.5 0.7 O1 B:CAC338 1.8 18.5 0.7 C1 B:CAC338 1.9 25.8 0.7 C2 B:CAC338 2.0 29.8 0.7 NA B:NA334 3.5 29.0 1.0 NE2 B:HIS138 3.8 13.3 1.0 O B:HOH824 3.9 36.2 1.0 CZ2 B:TRP33 4.2 27.6 1.0 OH B:TYR66 4.2 18.3 1.0 CE1 B:PHE221 4.2 15.0 1.0 CZ B:PHE221 4.3 15.9 1.0 CE2 B:TRP33 4.3 22.7 1.0 CH2 B:TRP33 4.3 28.4 1.0 CD2 B:HIS138 4.5 13.4 1.0 ND2 B:ASN169 4.6 16.5 1.0 CD1 B:PHE221 4.6 16.1 1.0 CD2 B:TRP33 4.7 23.9 1.0 CZ3 B:TRP33 4.7 29.4 1.0 CE2 B:PHE221 4.7 19.1 1.0 CE1 B:HIS138 4.7 14.5 1.0 O B:HOH839 4.7 43.5 1.0 NE1 B:TRP33 4.8 22.7 1.0 CE3 B:TRP33 4.8 23.5 1.0

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