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Sodium in PDB 8rja: Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum

Enzymatic activity of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum

All present enzymatic activity of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum:
1.2.7.12; 1.6.5.11; 3.5.2.5;

Protein crystallography data

The structure of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum, PDB code: 8rja was solved by O.N.Lemaire, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.38 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.627, 135.636, 149.902, 90, 90.49, 90
R / Rfree (%) 17.6 / 21

Other elements in 8rja:

The structure of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Iron (Fe) 48 atoms
Zinc (Zn) 4 atoms
Tungsten (W) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum (pdb code 8rja). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum, PDB code: 8rja:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8rja

Go back to Sodium Binding Sites List in 8rja
Sodium binding site 1 out of 4 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1110

b:47.0
occ:1.00
OE2 E:GLU232 3.8 77.7 1.0
CB E:ASP230 3.8 40.8 1.0
CD E:GLU232 4.0 74.7 1.0
CG E:GLU232 4.1 63.6 1.0
CA E:ASP230 4.1 42.2 1.0
CG E:ASP230 4.2 43.0 1.0
O E:ASP230 4.3 39.0 1.0
OD1 E:ASP230 4.4 40.3 1.0
C E:ASP230 4.6 40.5 1.0
OE1 E:GLU232 4.7 75.3 1.0
OD2 E:ASP230 4.8 44.2 1.0

Sodium binding site 2 out of 4 in 8rja

Go back to Sodium Binding Sites List in 8rja
Sodium binding site 2 out of 4 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na603

b:21.7
occ:1.00
O G:HOH915 2.4 24.1 1.0
CA G:GLY198 4.0 23.7 1.0
N G:GLY198 4.0 19.1 1.0
C G:ARG197 4.2 16.6 1.0
CB G:ASP201 4.2 19.0 1.0
N G:ASP201 4.2 20.2 1.0
O G:ARG197 4.3 24.1 1.0
CB G:ARG197 4.4 25.9 1.0
CA G:ASP201 4.5 19.2 1.0
C G:GLY198 4.5 22.1 1.0
C G:ASP200 4.6 18.9 1.0
N G:ASP200 4.7 17.4 1.0
CA G:ARG197 4.9 19.6 1.0
CG G:ASP201 4.9 22.5 1.0
N G:LEU199 5.0 21.8 1.0
O G:GLY198 5.0 20.5 1.0
CA G:ASP200 5.0 17.8 1.0

Sodium binding site 3 out of 4 in 8rja

Go back to Sodium Binding Sites List in 8rja
Sodium binding site 3 out of 4 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na511

b:47.4
occ:1.00
OD2 H:ASP409 3.4 61.8 1.0
CG H:ASP409 4.0 53.5 1.0
ND2 H:ASN26 4.1 31.1 1.0
OD1 H:ASP409 4.2 55.0 1.0
O H:GLU407 4.2 30.4 1.0
C H:GLU407 4.3 29.8 1.0
N H:SER408 4.3 29.7 1.0
CB H:GLU407 4.3 32.8 1.0
CA H:SER408 4.4 28.9 1.0
C H:SER408 4.4 31.7 1.0
N H:ASP409 4.5 34.1 1.0
O H:HOH793 4.8 26.7 1.0
O H:SER408 4.9 32.8 1.0
CB H:ASP409 5.0 46.5 1.0
CA H:GLU407 5.0 31.2 1.0

Sodium binding site 4 out of 4 in 8rja

Go back to Sodium Binding Sites List in 8rja
Sodium binding site 4 out of 4 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na1107

b:46.6
occ:1.00
OD1 K:ASP148 3.6 60.2 1.0
CG K:ASP148 3.7 59.1 1.0
OD2 K:ASP148 3.8 62.3 1.0
O K:HOH1203 4.0 42.4 1.0
CB K:VAL141 4.3 36.6 1.0
O K:LEU142 4.5 39.6 1.0
CB K:ASP148 4.6 52.9 1.0
CG2 K:VAL141 4.6 35.4 1.0
CG1 K:VAL141 4.7 41.5 1.0
NE2 K:GLN131 4.8 42.9 1.0
CA K:ALA143 4.9 38.1 1.0

Reference:

O.N.Lemaire, G.Wegener, T.Wagner. F420 Reduction As A Cellular Driver For Anaerobic Ethanotrophy To Be Published.
Page generated: Thu Oct 31 22:57:47 2024

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