Sodium in PDB 6zxu: Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged.

Protein crystallography data

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged., PDB code: 6zxu 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) 121.69 / 1.73
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.110, 170.958, 107.873, 90.00, 98.37, 90.00
R / Rfree (%) 16.3 / 19.4

Other elements in 6zxu:

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

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged. (pdb code 6zxu). 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., PDB code: 6zxu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6zxu

Go back to Sodium Binding Sites List in 6zxu
Sodium binding site 1 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:40.0
occ:1.00
O A:HOH835 2.3 26.2 1.0
O A:HOH1069 2.3 21.5 1.0
O A:HOH1174 2.5 39.3 1.0
O A:ASN571 2.5 17.9 1.0
O A:CYS568 3.0 14.1 1.0
C A:ASN571 3.7 15.8 1.0
C A:CYS568 3.9 15.8 1.0
O A:PRO569 4.0 13.9 1.0
CA A:PRO569 4.0 16.8 1.0
O A:LYS566 4.1 19.7 1.0
C A:PRO569 4.2 16.0 1.0
CB A:ASN571 4.2 18.0 1.0
CB A:ASN604 4.2 25.6 1.0
OD2 A:ASP599 4.2 21.1 1.0
CA A:ASN571 4.3 17.1 1.0
OD1 A:ASP599 4.3 24.1 1.0
N A:ASN571 4.3 13.3 1.0
N A:PRO569 4.3 15.8 1.0
ND2 A:ASN571 4.4 25.1 1.0
O A:MET567 4.4 20.4 1.0
CG A:ASN571 4.7 24.0 1.0
C A:MET567 4.7 19.4 1.0
CG A:ASP599 4.7 21.6 1.0
N A:ARG572 4.7 17.8 1.0
N A:GLY605 4.8 21.4 1.0
N A:CYS568 4.9 18.0 1.0
C A:ASN604 4.9 20.9 1.0
CG A:ASN604 4.9 28.0 1.0

Sodium binding site 2 out of 3 in 6zxu

Go back to Sodium Binding Sites List in 6zxu
Sodium binding site 2 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na704

b:44.0
occ:1.00
O B:HOH1010 2.3 24.1 1.0
O B:HOH1094 2.4 41.3 1.0
O B:HOH1045 2.5 27.8 1.0
O B:ASN571 2.6 18.1 1.0
O B:HOH1289 2.8 39.3 1.0
O B:CYS568 3.1 15.4 1.0
C B:ASN571 3.7 19.6 1.0
C B:CYS568 4.0 18.5 1.0
O B:LYS566 4.1 24.3 1.0
CB B:ASN604 4.1 30.2 1.0
O B:PRO569 4.2 20.2 1.0
CA B:PRO569 4.2 20.4 1.0
OD2 B:ASP599 4.3 24.8 1.0
CB B:ASN571 4.3 19.1 1.0
ND2 B:ASN571 4.4 29.1 1.0
C B:PRO569 4.4 19.5 1.0
CA B:ASN571 4.4 18.5 1.0
N B:ASN571 4.5 16.0 1.0
N B:PRO569 4.6 16.5 1.0
OD1 B:ASP599 4.6 27.6 1.0
O B:MET567 4.6 20.2 1.0
N B:GLY605 4.7 26.6 1.0
CG B:ASN571 4.7 22.6 1.0
N B:ARG572 4.8 17.5 1.0
C B:MET567 4.8 20.7 1.0
C B:ASN604 4.8 26.5 1.0
CG B:ASP599 4.9 28.3 1.0
CG B:ASN604 4.9 30.8 1.0

Sodium binding site 3 out of 3 in 6zxu

Go back to Sodium Binding Sites List in 6zxu
Sodium binding site 3 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na704

b:37.2
occ:1.00
O C:ASN571 2.4 24.5 1.0
O C:HOH879 2.5 30.6 1.0
O C:HOH913 2.7 28.8 1.0
O C:CYS568 2.7 20.4 1.0
O C:HOH1165 2.7 40.2 1.0
C C:ASN571 3.4 25.8 1.0
C C:CYS568 3.7 21.7 1.0
O C:PRO569 3.9 21.8 1.0
CB C:ASN571 3.9 25.9 1.0
O C:LYS566 3.9 24.0 1.0
CA C:PRO569 3.9 20.7 1.0
CA C:ASN571 4.0 23.1 1.0
C C:PRO569 4.1 21.0 1.0
N C:ASN571 4.1 20.6 1.0
N C:PRO569 4.3 19.1 1.0
ND2 C:ASN571 4.3 37.7 1.0
OD1 C:ASP599 4.4 26.9 1.0
OD2 C:ASP599 4.4 28.0 1.0
O C:MET567 4.4 23.8 1.0
CG C:ASN571 4.5 27.9 1.0
CB C:ASN604 4.5 30.1 1.0
C C:MET567 4.6 25.3 1.0
N C:ARG572 4.6 22.5 1.0
N C:CYS568 4.8 25.0 1.0
CA C:CYS568 4.9 22.5 1.0
CG C:ASP599 4.9 34.0 1.0
N C:TRP570 4.9 18.9 1.0
CA C:ARG572 5.0 24.0 1.0

Reference:

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
Page generated: Tue Dec 15 17:14:31 2020

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