Zinc 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
Sodium (Na) 4 atoms
Iron (Fe) 48 atoms
Tungsten (W) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum, PDB code: 8rja:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8rja

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Zinc 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 Zinc with other atoms in the Zn 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
A:Zn601

b:42.7
occ:1.00
 OD1 A:ASP383 2.1 19.2 1.0
NE2 A:HIS60 2.3 19.0 1.0
NE2 A:HIS58 2.3 19.0 1.0
OQ1 A:KCX180 2.8 31.3 1.0
CG A:ASP383 3.1 17.1 1.0
ZN A:ZN602 3.1 33.6 1.0
CE1 A:HIS60 3.2 18.7 1.0
CD2 A:HIS58 3.3 18.4 1.0
OD2 A:ASP383 3.3 24.2 1.0
CD2 A:HIS60 3.4 18.5 1.0
CE1 A:HIS58 3.4 18.1 1.0
CX A:KCX180 3.5 28.1 1.0
OQ2 A:KCX180 3.5 26.0 1.0
CD2 A:HIS269 3.8 17.4 1.0
CB A:ALA117 4.1 21.7 1.0
ND2 A:ASN386 4.1 16.0 1.0
NE2 A:HIS269 4.2 18.8 1.0
ND1 A:HIS60 4.3 19.6 1.0
CG A:HIS60 4.4 17.9 1.0
CB A:ASP383 4.5 18.3 1.0
CG A:HIS58 4.5 17.0 1.0
ND1 A:HIS58 4.5 19.3 1.0
O A:HOH991 4.5 29.9 1.0
NZ A:KCX180 4.5 21.0 1.0
O A:HOH711 4.7 19.4 1.0
O A:MET315 4.8 20.5 1.0
CA A:ASP383 4.9 14.8 1.0
O A:ASP383 4.9 14.9 1.0
CG A:ASN386 4.9 17.0 1.0

Zinc binding site 2 out of 4 in 8rja

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Zinc 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 Zinc with other atoms in the Zn 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
A:Zn602

b:33.6
occ:1.00
 OQ2 A:KCX180 2.2 26.0 1.0
NE2 A:HIS269 2.3 18.8 1.0
ND1 A:HIS233 2.5 19.7 1.0
O A:HOH991 2.9 29.9 1.0
CX A:KCX180 3.0 28.1 1.0
CD2 A:HIS269 3.1 17.4 1.0
OQ1 A:KCX180 3.1 31.3 1.0
ZN A:ZN601 3.1 42.7 1.0
CE1 A:HIS233 3.3 19.8 1.0
CE1 A:HIS269 3.4 18.1 1.0
CG A:HIS233 3.5 21.1 1.0
OG1 A:THR316 3.7 28.2 1.0
CB A:HIS233 3.8 18.5 1.0
O A:HOH711 4.1 19.4 1.0
OD2 A:ASP383 4.2 24.2 1.0
CG A:HIS269 4.3 17.0 1.0
NZ A:KCX180 4.3 21.0 1.0
CB A:THR316 4.3 19.1 1.0
ND1 A:HIS269 4.4 18.2 1.0
NE2 A:HIS58 4.5 19.0 1.0
NE2 A:HIS233 4.5 19.8 1.0
OD1 A:ASP383 4.5 19.2 1.0
CG2 A:THR268 4.6 15.5 1.0
CD2 A:HIS233 4.6 19.7 1.0
CG A:ASP383 4.7 17.1 1.0
CE1 A:HIS58 4.8 18.1 1.0
NE2 A:HIS60 4.8 19.0 1.0
CG2 A:VAL182 4.9 18.7 1.0
CE A:KCX180 5.0 14.7 1.0

Zinc binding site 3 out of 4 in 8rja

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Zinc 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 Zinc with other atoms in the Zn 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
G:Zn601

b:42.7
occ:1.00
 NE2 G:HIS60 2.3 22.7 1.0
NE2 G:HIS58 2.3 22.7 1.0
OD1 G:ASP383 2.4 20.2 1.0
OQ2 G:KCX180 2.6 21.4 1.0
CE1 G:HIS60 3.0 22.1 1.0
ZN G:ZN602 3.2 33.2 1.0
CE1 G:HIS58 3.2 21.2 1.0
CX G:KCX180 3.2 26.9 1.0
CD2 G:HIS58 3.3 16.6 1.0
CG G:ASP383 3.3 22.1 1.0
CD2 G:HIS60 3.4 21.1 1.0
OQ1 G:KCX180 3.4 27.4 1.0
OD2 G:ASP383 3.6 22.7 1.0
CD2 G:HIS269 3.9 16.9 1.0
CB G:ALA117 3.9 20.2 1.0
ND1 G:HIS60 4.2 19.5 1.0
NE2 G:HIS269 4.2 18.5 1.0
NZ G:KCX180 4.3 20.6 1.0
ND2 G:ASN386 4.3 14.0 1.0
CG G:HIS60 4.4 17.4 1.0
ND1 G:HIS58 4.4 19.5 1.0
CG G:HIS58 4.4 18.6 1.0
O G:HOH709 4.5 15.9 1.0
CB G:ASP383 4.7 15.5 1.0
O G:MET315 4.9 18.8 1.0

Zinc binding site 4 out of 4 in 8rja

Go back to Zinc Binding Sites List in 8rja
Zinc 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 Zinc with other atoms in the Zn 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
G:Zn602

b:33.2
occ:1.00
 OQ1 G:KCX180 2.1 27.4 1.0
NE2 G:HIS269 2.4 18.5 1.0
ND1 G:HIS233 2.4 14.6 1.0
CX G:KCX180 3.0 26.9 1.0
OQ2 G:KCX180 3.1 21.4 1.0
ZN G:ZN601 3.2 42.7 1.0
CD2 G:HIS269 3.2 16.9 1.0
CE1 G:HIS233 3.3 16.2 1.0
CE1 G:HIS269 3.4 14.6 1.0
CG G:HIS233 3.5 16.7 1.0
OG1 G:THR316 3.7 25.6 1.0
CB G:HIS233 3.7 18.7 1.0
O G:HOH709 3.8 15.9 1.0
NZ G:KCX180 4.3 20.6 1.0
CG G:HIS269 4.3 14.5 1.0
OD2 G:ASP383 4.3 22.7 1.0
CB G:THR316 4.3 19.9 1.0
ND1 G:HIS269 4.4 12.4 1.0
NE2 G:HIS233 4.5 16.8 1.0
NE2 G:HIS58 4.5 22.7 1.0
CD2 G:HIS233 4.6 14.9 1.0
CG2 G:THR268 4.6 18.8 1.0
OD1 G:ASP383 4.6 20.2 1.0
CE1 G:HIS58 4.8 21.2 1.0
CG2 G:VAL182 4.8 17.5 1.0
NE2 G:HIS60 4.9 22.7 1.0
CG G:ASP383 4.9 22.1 1.0
CE G:KCX180 4.9 14.4 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 10:31:24 2024

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