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

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

Sodium 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 Sodium with other atoms in the Na 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:Na334 b:35.0 occ:1.00 O1 A:CAC337 2.4 17.7 0.6 OG A:SER168 2.7 16.9 1.0 OE1 A:GLN193 2.8 18.4 1.0 AS A:CAC337 3.4 30.2 0.6 CD A:GLN193 3.6 16.6 1.0 NE2 A:HIS138 3.6 14.8 1.0 CD2 A:HIS138 3.6 15.3 1.0 CB A:SER168 3.7 14.6 1.0 O2 A:CAC337 3.8 18.6 0.6 C2 A:CAC337 3.8 24.2 0.6 CE A:LYS97 3.8 15.4 1.0 ND2 A:ASN169 3.9 18.4 1.0 CE2 A:PHE221 3.9 16.6 0.7 CG A:GLN193 4.0 12.7 1.0 CD2 A:PHE221 4.0 15.9 0.7 O A:HOH771 4.1 30.4 0.6 CD A:LYS97 4.2 15.0 1.0 CD1 A:PHE221 4.4 18.0 0.3 NZ A:LYS97 4.4 16.1 1.0 CZ A:PHE221 4.5 15.4 0.7 O A:GLN193 4.6 14.6 1.0 NE2 A:GLN193 4.6 13.7 1.0 OH A:TYR66 4.6 20.4 1.0 CB A:GLN193 4.7 13.7 1.0 CE1 A:PHE221 4.7 16.7 0.3 O A:HIS138 4.7 14.1 1.0 CG A:ASN169 4.7 18.6 1.0 CG A:PHE221 4.8 15.3 0.7 CE1 A:HIS138 4.8 16.9 1.0 OD1 A:ASN169 4.8 22.4 1.0 CG A:PHE221 4.8 15.7 0.3 CG A:HIS138 4.9 15.2 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na334 b:29.0 occ:1.00 O2 B:CAC338 2.4 16.5 0.7 OG B:SER168 2.8 15.6 1.0 OE1 B:GLN193 2.8 17.5 1.0 AS B:CAC338 3.5 27.5 0.7 CD B:GLN193 3.6 17.3 1.0 CD2 B:HIS138 3.6 13.4 1.0 NE2 B:HIS138 3.6 13.3 1.0 CE B:LYS97 3.7 12.2 1.0 CB B:SER168 3.8 13.2 1.0 O1 B:CAC338 3.8 18.5 0.7 C1 B:CAC338 3.8 25.8 0.7 ND2 B:ASN169 3.9 16.5 1.0 CG B:GLN193 4.0 13.5 1.0 CD B:LYS97 4.0 12.6 1.0 CE2 B:PHE221 4.2 19.1 1.0 CD2 B:PHE221 4.2 18.6 1.0 NZ B:LYS97 4.3 12.6 1.0 OH B:TYR66 4.5 18.3 1.0 O B:HOH839 4.5 43.5 1.0 NE2 B:GLN193 4.5 14.7 1.0 O B:GLN193 4.6 15.2 1.0 O B:HIS138 4.6 12.4 1.0 CB B:GLN193 4.6 13.1 1.0 CZ B:PHE221 4.8 15.9 1.0 CG B:ASN169 4.8 16.3 1.0 CG B:HIS138 4.8 12.2 1.0 CE1 B:HIS138 4.9 14.5 1.0 CG B:PHE221 4.9 17.6 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