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

Protein crystallography data

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged., PDB code: 6zxx 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) 106.58 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 180.182, 170.391, 107.957, 90.00, 99.16, 90.00
R / Rfree (%) 18.2 / 21.8

Other elements in 6zxx:

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

Cobalt (Co) 3 atoms
Bromine (Br) 12 atoms
Iron (Fe) 24 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 6zxx

Go back to Sodium Binding Sites List in 6zxx
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:36.0
occ:1.00
O A:HOH994 2.2 18.1 1.0
O A:HOH1026 2.3 25.4 1.0
O A:ASN571 2.5 17.2 1.0
O A:HOH912 2.5 25.4 1.0
O A:HOH956 2.7 27.0 1.0
O A:CYS568 3.4 15.2 1.0
C A:ASN571 3.7 17.4 1.0
CB A:ASN604 4.0 25.0 1.0
O A:LYS566 4.1 17.8 1.0
O A:HOH808 4.2 35.0 1.0
O A:PRO569 4.2 17.6 1.0
C A:CYS568 4.3 17.0 1.0
CB A:ASN571 4.3 19.3 1.0
OD1 A:ASP599 4.3 24.5 1.0
OD2 A:ASP599 4.4 17.7 1.0
ND2 A:ASN571 4.4 21.6 1.0
CA A:PRO569 4.4 16.5 1.0
CA A:ASN571 4.4 18.3 1.0
C A:PRO569 4.5 15.8 1.0
N A:GLY605 4.6 25.1 1.0
N A:ASN571 4.6 18.0 1.0
N A:ARG572 4.7 17.8 1.0
C A:ASN604 4.7 25.3 1.0
CG A:ASN571 4.7 20.2 1.0
CG A:ASN604 4.8 23.5 1.0
CG A:ASP599 4.8 21.5 1.0
N A:PRO569 4.8 16.6 1.0
CA A:ASN604 4.9 24.5 1.0
CA A:ARG572 4.9 17.9 1.0
OE1 A:GLU409 4.9 44.4 1.0
O A:MET567 4.9 20.1 1.0
CG A:ARG572 5.0 18.1 1.0

Sodium binding site 2 out of 3 in 6zxx

Go back to Sodium Binding Sites List in 6zxx
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:44.3
occ:1.00
O B:HOH852 2.4 31.2 1.0
O B:ASN571 2.7 21.0 1.0
O B:HOH1004 2.8 27.1 1.0
O B:CYS568 3.4 23.8 1.0
O B:LYS566 3.6 29.3 1.0
C B:ASN571 3.9 21.6 1.0
ND2 B:ASN571 4.1 28.6 1.0
CB B:ASN604 4.1 29.8 1.0
N B:GLY605 4.2 27.2 1.0
CB B:ASN571 4.2 22.2 1.0
C B:CYS568 4.4 23.0 1.0
OE1 B:GLU409 4.4 56.9 1.0
C B:ASN604 4.5 28.7 1.0
CA B:ASN571 4.5 21.4 1.0
CG B:ASN571 4.6 25.4 1.0
OD2 B:ASP599 4.6 23.9 1.0
OE2 B:GLU409 4.7 54.9 1.0
O B:MET567 4.7 29.0 1.0
C B:MET567 4.7 27.3 1.0
C B:LYS566 4.8 25.8 1.0
CA B:PRO569 4.8 20.5 1.0
O B:PRO569 4.8 19.9 1.0
OD1 B:ASP599 4.8 29.3 1.0
CA B:ASN604 4.8 30.0 1.0
CA B:GLY605 4.8 28.3 1.0
N B:ASN571 4.8 20.8 1.0
C B:PRO569 4.9 19.9 1.0
N B:CYS568 5.0 26.5 1.0
N B:ARG572 5.0 21.5 1.0
CD B:GLU409 5.0 47.9 1.0

Sodium binding site 3 out of 3 in 6zxx

Go back to Sodium Binding Sites List in 6zxx
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:Na804

b:55.3
occ:1.00
O C:ASN575 2.3 29.5 1.0
O C:HOH954 2.3 33.6 1.0
O C:HOH984 2.4 33.0 1.0
O C:HOH957 2.4 30.9 1.0
C C:ASN575 3.5 24.9 1.0
O C:CYS572 3.9 27.3 1.0
O C:HOH903 4.0 35.9 1.0
CB C:ASN608 4.1 27.2 1.0
ND2 C:ASN575 4.3 32.8 1.0
OE2 C:GLU413 4.3 57.1 1.0
O C:LYS570 4.3 26.7 1.0
CB C:ASN575 4.4 27.1 1.0
CA C:ASN575 4.5 24.9 1.0
N C:ARG576 4.5 24.9 1.0
O C:PRO573 4.5 21.8 1.0
CA C:ARG576 4.6 26.0 1.0
N C:GLY609 4.6 34.9 1.0
OH C:TYR409 4.6 33.9 1.0
CG C:ASN575 4.7 29.0 1.0
CE1 C:TYR409 4.7 30.8 1.0
OD1 C:ASP603 4.7 24.1 1.0
CG C:ASN608 4.8 26.3 1.0
N C:ASN575 4.8 23.1 1.0
CG C:ARG576 4.8 25.7 1.0
C C:ASN608 4.9 32.4 1.0
C C:CYS572 4.9 24.0 1.0
OD2 C:ASP603 4.9 26.3 1.0
CA C:PRO573 4.9 22.7 1.0
CA C:ASN608 4.9 30.9 1.0
C C:PRO573 4.9 21.8 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 17:15:16 2020

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