Sodium in PDB 6qsi: Pseudomonas Fluorescens Pf-5 Thiamine Diphosphate-Dependent 4- Hydroxybenzoylformate Decarboxylase

All present enzymatic activity of Pseudomonas Fluorescens Pf-5 Thiamine Diphosphate-Dependent 4- Hydroxybenzoylformate Decarboxylase:
4.1.1.7;

The structure of Pseudomonas Fluorescens Pf-5 Thiamine Diphosphate-Dependent 4- Hydroxybenzoylformate Decarboxylase, PDB code: 6qsi was solved by R.C.Wilkinson, V.Fulop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.49 / 1.69
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.720, 130.720, 180.540, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18

The binding sites of Sodium atom in the Pseudomonas Fluorescens Pf-5 Thiamine Diphosphate-Dependent 4- Hydroxybenzoylformate Decarboxylase (pdb code 6qsi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pseudomonas Fluorescens Pf-5 Thiamine Diphosphate-Dependent 4- Hydroxybenzoylformate Decarboxylase, PDB code: 6qsi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pseudomonas Fluorescens Pf-5 Thiamine Diphosphate-Dependent 4- Hydroxybenzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pseudomonas Fluorescens Pf-5 Thiamine Diphosphate-Dependent 4- Hydroxybenzoylformate Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:7.9 occ:1.00 OD1 A:ASP428 2.2 19.9 1.0 OD1 A:ASN455 2.3 16.7 1.0 O3B A:TPP601 2.3 19.3 1.0 O2A A:TPP601 2.3 18.4 1.0 O A:THR457 2.3 18.1 1.0 O A:HOH732 2.4 18.6 1.0 CG A:ASN455 3.1 17.5 1.0 CG A:ASP428 3.4 19.0 1.0 ND2 A:ASN455 3.4 17.0 1.0 PA A:TPP601 3.4 18.8 1.0 PB A:TPP601 3.5 19.1 1.0 C A:THR457 3.5 18.6 1.0 O3A A:TPP601 3.7 17.8 1.0 N A:THR457 4.1 18.9 1.0 OD2 A:ASP428 4.1 20.1 1.0 O7 A:TPP601 4.1 18.8 1.0 N A:ASP428 4.2 16.2 1.0 N A:GLY429 4.3 18.6 1.0 N A:GLY459 4.3 18.9 1.0 CA A:THR457 4.4 18.8 1.0 O1B A:TPP601 4.4 19.8 1.0 N A:ASN455 4.4 17.2 1.0 CB A:ASN455 4.4 17.7 1.0 N A:TYR458 4.5 18.3 1.0 O A:LEU453 4.5 17.8 1.0 O A:HOH763 4.6 19.1 1.0 N A:GLY456 4.6 18.0 1.0 CB A:ASP428 4.6 18.6 1.0 CA A:TYR458 4.6 18.0 1.0 CG2 A:THR457 4.6 19.1 1.0 O2B A:TPP601 4.7 19.0 1.0 O1A A:TPP601 4.7 18.7 1.0 CA A:ASP428 4.7 17.6 1.0 CA A:ASN455 4.7 18.1 1.0 C A:ASN455 4.9 18.4 1.0 CA A:GLY427 4.9 16.4 1.0 C A:GLY427 5.0 16.6 1.0 C A:ASP428 5.0 18.6 1.0

Sodium binding site 2 out of 2 in the Pseudomonas Fluorescens Pf-5 Thiamine Diphosphate-Dependent 4- Hydroxybenzoylformate Decarboxylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pseudomonas Fluorescens Pf-5 Thiamine Diphosphate-Dependent 4- Hydroxybenzoylformate Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:8.6 occ:1.00 O1A B:TPP601 2.2 19.8 1.0 OD1 B:ASP428 2.2 20.4 1.0 O B:THR457 2.3 20.1 1.0 O1B B:TPP601 2.3 19.9 1.0 OD1 B:ASN455 2.3 18.1 1.0 O B:HOH729 2.4 20.8 1.0 CG B:ASN455 3.1 20.1 1.0 PA B:TPP601 3.4 20.1 1.0 CG B:ASP428 3.4 19.8 1.0 ND2 B:ASN455 3.5 20.6 1.0 PB B:TPP601 3.5 21.0 1.0 C B:THR457 3.5 19.9 1.0 O3A B:TPP601 3.6 19.9 1.0 OD2 B:ASP428 4.0 20.1 1.0 N B:THR457 4.0 19.4 1.0 O7 B:TPP601 4.1 18.3 1.0 N B:ASP428 4.1 16.9 1.0 N B:GLY429 4.3 17.6 1.0 N B:GLY459 4.3 19.6 1.0 O3B B:TPP601 4.4 22.3 1.0 CA B:THR457 4.4 20.3 1.0 N B:ASN455 4.4 19.7 1.0 CB B:ASN455 4.5 20.7 1.0 N B:TYR458 4.5 19.4 1.0 O B:HOH751 4.5 22.7 1.0 O B:LEU453 4.6 21.1 1.0 O2B B:TPP601 4.6 20.2 1.0 CA B:TYR458 4.6 18.6 1.0 CB B:ASP428 4.7 18.7 1.0 N B:GLY456 4.7 20.3 1.0 O2A B:TPP601 4.7 19.3 1.0 CA B:ASP428 4.7 18.0 1.0 CA B:ASN455 4.7 20.0 1.0 CG2 B:THR457 4.8 20.8 1.0 C B:ASN455 4.9 20.8 1.0 CA B:GLY427 4.9 18.8 1.0 C B:GLY427 4.9 18.0 1.0 C B:ASP428 5.0 18.1 1.0

Z.Wei, R.C.Wilkinson, G.M.M.Rashid, D.Brown, V.Fulop, T.D.H.Bugg. Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes Fromrhodococcus JOSTIIRHA1 Andpseudomonas Fluorescenspf-5 Involved in Degradation of Aryl C2LIGNIN Degradation Fragments. Biochemistry V. 58 5281 2019.
ISSN: ISSN 0006-2960
PubMed: 30946572
DOI: 10.1021/ACS.BIOCHEM.9B00177