Sodium in PDB 6zy0: Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant, PDB code: 6zy0 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)	106.66 / 2.13
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.346, 169.569, 107.799, 90.00, 98.33, 90.00
R / Rfree (%)	18.6 / 22.2

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant also contains other interesting chemical elements:

Cobalt	(Co)	3 atoms
Iron	(Fe)	24 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant (pdb code 6zy0). 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, K488Q Variant, PDB code: 6zy0:
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, K488Q Variant


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, K488Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:38.2 occ:1.00 O A:ASN571 3.0 31.2 1.0 O A:CYS568 3.3 26.9 1.0 O A:LYS566 3.8 34.3 1.0 CB A:ASN604 3.9 32.8 1.0 OD2 A:ASP599 4.0 30.0 1.0 C A:ASN571 4.1 27.8 1.0 C A:CYS568 4.2 26.9 1.0 CB A:ASN571 4.2 28.6 1.0 N A:GLY605 4.2 31.7 1.0 OD1 A:ASP599 4.3 30.5 1.0 CA A:PRO569 4.3 29.5 1.0 ND2 A:ASN571 4.4 32.1 1.0 C A:ASN604 4.4 33.1 1.0 O A:MET567 4.4 34.3 1.0 O A:PRO569 4.5 28.8 1.0 CG A:ASP599 4.6 32.5 1.0 CA A:ASN571 4.6 26.0 1.0 C A:PRO569 4.6 26.1 1.0 C A:MET567 4.7 30.0 1.0 N A:PRO569 4.7 24.8 1.0 CA A:ASN604 4.7 32.2 1.0 N A:ASN571 4.7 25.6 1.0 CG A:ASN571 4.8 30.2 1.0 CA A:GLY605 4.8 34.9 1.0 CG A:ASN604 4.8 32.3 1.0 O A:ASN604 4.9 36.2 1.0 N A:CYS568 5.0 31.7 1.0

Sodium binding site 2 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


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, K488Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na704 b:41.9 occ:1.00 O B:ASN571 3.0 34.5 1.0 O B:CYS568 3.0 31.6 1.0 OD2 B:ASP599 3.7 32.8 1.0 OD1 B:ASP599 3.7 31.7 1.0 CA B:PRO569 3.8 28.0 1.0 CB B:ASN604 3.8 37.4 1.0 C B:CYS568 3.9 29.2 1.0 O B:PRO569 4.0 29.2 1.0 C B:ASN571 4.1 33.5 1.0 CG B:ASP599 4.1 34.1 1.0 C B:PRO569 4.1 26.1 1.0 N B:PRO569 4.3 24.6 1.0 O B:LYS566 4.4 34.9 1.0 CB B:ASN571 4.4 26.2 1.0 N B:ASN571 4.5 25.4 1.0 O B:MET567 4.6 35.1 1.0 CA B:ASN571 4.6 27.0 1.0 C B:ASN604 4.6 38.1 1.0 CG B:ASN604 4.7 37.4 1.0 N B:GLY605 4.7 39.0 1.0 CA B:ASN604 4.8 39.7 1.0 C B:MET567 4.8 33.1 1.0 O B:ASN604 4.9 42.3 1.0 ND2 B:ASN571 4.9 35.3 1.0 ND2 B:ASN604 4.9 38.8 1.0

Sodium binding site 3 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


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, K488Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Na704 b:51.1 occ:1.00 O C:ASN571 2.9 44.7 1.0 O C:LYS566 3.6 37.4 1.0 O C:CYS568 3.7 40.3 1.0 C C:ASN571 4.0 40.6 1.0 ND2 C:ASN571 4.0 42.9 1.0 N C:GLY605 4.1 47.0 1.0 CB C:ASN571 4.1 31.8 1.0 CB C:ASN604 4.2 41.4 1.0 OE1 C:GLU409 4.4 61.3 1.0 CG C:ASN571 4.4 35.3 1.0 C C:ASN604 4.5 43.0 1.0 CA C:ASN571 4.6 35.3 1.0 CA C:GLY605 4.6 50.1 1.0 C C:CYS568 4.7 40.2 1.0 OD2 C:ASP599 4.7 45.6 1.0 C C:LYS566 4.8 34.2 1.0 CA C:ASN604 4.9 45.2 1.0 CE1 C:TYR405 4.9 45.7 1.0 O C:MET567 4.9 48.0 1.0 N C:ASN571 4.9 32.7 1.0 OD1 C:ASP599 4.9 41.7 1.0 C C:MET567 4.9 43.6 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