Sodium in PDB 6zy1: Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid, PDB code: 6zy1 was solved by D.Leys, T.Halliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	106.00 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	175.871, 170.104, 107.651, 90.00, 98.35, 90.00
R / Rfree (%)	17.7 / 21.1

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid also contains other interesting chemical elements:

Cobalt	(Co)	3 atoms
Bromine	(Br)	9 atoms
Iron	(Fe)	24 atoms

The binding sites of Sodium atom in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid (pdb code 6zy1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid, PDB code: 6zy1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:25.5 occ:1.00 O A:HOH1133 2.6 23.4 1.0 O A:HOH900 2.7 20.9 1.0 O A:HOH1097 2.8 22.8 1.0 O A:ASN571 2.9 15.6 1.0 O A:CYS568 3.1 12.8 1.0 C A:CYS568 3.9 14.7 1.0 O A:LYS566 4.0 18.4 1.0 CB A:ASN604 4.0 17.2 1.0 CA A:PRO569 4.0 17.0 1.0 C A:ASN571 4.1 16.9 1.0 OD2 A:ASP599 4.1 17.7 1.0 OD1 A:ASP599 4.1 14.8 1.0 O A:MET567 4.2 16.8 1.0 O A:PRO569 4.3 14.6 1.0 CB A:ASN571 4.3 14.1 1.0 N A:GLY605 4.3 14.0 1.0 N A:PRO569 4.4 13.9 1.0 C A:PRO569 4.4 14.1 1.0 C A:MET567 4.5 17.4 1.0 C A:ASN604 4.5 15.7 1.0 CG A:ASP599 4.6 15.9 1.0 O A:HOH829 4.6 24.5 1.0 CA A:ASN571 4.6 15.8 1.0 ND2 A:ASN571 4.6 18.2 1.0 N A:ASN571 4.7 16.7 1.0 CA A:ASN604 4.8 15.9 1.0 N A:CYS568 4.8 19.8 1.0 CG A:ASN604 4.8 16.9 1.0 CA A:GLY605 4.9 20.5 1.0 CG A:ASN571 4.9 16.5 1.0 O A:ASN604 4.9 16.6 1.0

Sodium binding site 2 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na704 b:34.7 occ:1.00 O B:HOH1002 2.4 21.9 1.0 O B:ASN571 2.4 18.0 1.0 O B:HOH1034 2.5 22.4 1.0 O B:HOH863 2.8 28.3 1.0 O B:CYS568 3.4 20.4 1.0 C B:ASN571 3.5 18.5 1.0 O B:LYS566 4.0 16.9 1.0 CB B:ASN571 4.0 14.9 1.0 O B:HOH803 4.1 26.3 1.0 CB B:ASN604 4.2 20.9 1.0 CA B:ASN571 4.2 18.0 1.0 C B:CYS568 4.4 19.3 1.0 O B:PRO569 4.4 18.3 1.0 N B:ASN571 4.4 16.6 1.0 ND2 B:ASN571 4.4 18.1 1.0 OD1 B:ASP599 4.4 18.2 1.0 CA B:PRO569 4.5 18.6 1.0 CG B:ASN571 4.5 18.7 1.0 N B:ARG572 4.6 19.1 1.0 C B:PRO569 4.6 17.3 1.0 N B:GLY605 4.6 19.4 1.0 OD2 B:ASP599 4.8 18.0 1.0 CA B:ARG572 4.8 17.1 1.0 C B:ASN604 4.9 20.1 1.0 N B:PRO569 4.9 15.0 1.0 CG B:ASN604 4.9 25.0 1.0 OH B:TYR405 5.0 26.0 1.0 CE1 B:TYR405 5.0 22.2 1.0

Sodium binding site 3 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Na704 b:32.4 occ:1.00 O C:ASN571 2.4 23.8 1.0 O C:HOH952 2.5 28.2 1.0 O C:HOH871 2.6 24.0 1.0 O C:CYS568 3.4 22.4 1.0 C C:ASN571 3.4 23.8 1.0 O C:PRO569 3.8 20.9 1.0 CB C:ASN571 4.1 16.6 1.0 CA C:ASN571 4.1 21.6 1.0 CA C:PRO569 4.2 21.6 1.0 C C:PRO569 4.2 24.0 1.0 CB C:ASN604 4.2 22.7 1.0 N C:ASN571 4.2 17.5 1.0 C C:CYS568 4.3 22.9 1.0 O C:LYS566 4.3 17.9 1.0 OD1 C:ASP599 4.4 25.3 1.0 N C:ARG572 4.4 22.9 1.0 OD2 C:ASP599 4.5 24.1 1.0 ND2 C:ASN571 4.6 23.2 1.0 CA C:ARG572 4.6 16.8 1.0 CG C:ASN571 4.6 19.7 1.0 N C:PRO569 4.7 20.1 1.0 CG C:ARG572 4.7 21.3 1.0 CG C:ASN604 4.8 21.3 1.0 N C:GLY605 4.9 22.9 1.0 O C:HOH812 4.9 26.4 1.0 CG C:ASP599 4.9 26.1 1.0 O C:MET567 4.9 21.4 1.0

T.Halliwell, K.Fisher, K.A.P.Payne, S.E.J.Rigby, D.Leys. Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope. Microorganisms V. 8 2020.
ISSN: ISSN 2076-2607
PubMed: 32887524
DOI: 10.3390/MICROORGANISMS8091344