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Nickel in PDB 8riu: Crystal Structure of the F420-Reducing Carbon Monoxide Dehydrogenase Component From the Ethanotroph Candidatus Ethanoperedens Thermophilum

Enzymatic activity of Crystal Structure of the F420-Reducing Carbon Monoxide Dehydrogenase Component From the Ethanotroph Candidatus Ethanoperedens Thermophilum

All present enzymatic activity of Crystal Structure of the F420-Reducing Carbon Monoxide Dehydrogenase Component From the Ethanotroph Candidatus Ethanoperedens Thermophilum:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of the F420-Reducing Carbon Monoxide Dehydrogenase Component From the Ethanotroph Candidatus Ethanoperedens Thermophilum, PDB code: 8riu 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) 39.80 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.07, 159.213, 191.444, 90, 90, 90
R / Rfree (%) 16.5 / 18.7

Other elements in 8riu:

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

Chlorine (Cl) 1 atom
Potassium (K) 2 atoms
Iron (Fe) 60 atoms

Nickel Binding Sites:

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

Nickel binding site 1 out of 2 in 8riu

Go back to Nickel Binding Sites List in 8riu
Nickel binding site 1 out of 2 in the Crystal Structure of the F420-Reducing Carbon Monoxide Dehydrogenase Component From the Ethanotroph Candidatus Ethanoperedens Thermophilum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the F420-Reducing Carbon Monoxide Dehydrogenase Component From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni812

b:40.7
occ:1.00
NI A:XCC812 0.0 40.7 1.0
SG A:CYS572 2.0 37.3 1.0
S4 A:XCC812 2.1 38.0 1.0
S1 A:XCC812 2.4 34.6 1.0
FE2 A:XCC812 2.6 38.1 1.0
FE3 A:XCC812 2.9 33.9 1.0
S3 A:XCC812 3.2 35.2 1.0
CB A:CYS572 3.3 36.4 1.0
FE4 A:XCC812 3.4 31.9 1.0
FE1 A:XCC812 3.4 31.2 1.0
S2 A:XCC812 3.8 36.8 1.0
NE2 A:HIS242 4.2 37.3 1.0
NZ A:LYS622 4.3 38.3 1.0
O A:HOH987 4.5 32.7 1.0
CA A:CYS572 4.7 39.4 1.0
SG A:CYS270 4.7 34.5 1.0
SG A:CYS508 4.8 32.5 1.0
OG A:SER620 4.9 32.6 1.0

Nickel binding site 2 out of 2 in 8riu

Go back to Nickel Binding Sites List in 8riu
Nickel binding site 2 out of 2 in the Crystal Structure of the F420-Reducing Carbon Monoxide Dehydrogenase Component From the Ethanotroph Candidatus Ethanoperedens Thermophilum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the F420-Reducing Carbon Monoxide Dehydrogenase Component From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni806

b:43.0
occ:1.00
NI D:XCC806 0.0 43.0 1.0
SG D:CYS572 2.1 42.6 1.0
S1 D:XCC806 2.3 36.7 1.0
S4 D:XCC806 2.6 40.0 1.0
FE2 D:XCC806 2.7 41.6 1.0
FE3 D:XCC806 2.9 32.4 1.0
FE1 D:XCC806 3.4 34.5 1.0
CB D:CYS572 3.4 34.9 1.0
S3 D:XCC806 3.5 39.1 1.0
FE4 D:XCC806 3.5 34.3 1.0
S2 D:XCC806 3.8 38.1 1.0
NE2 D:HIS242 4.2 37.0 1.0
O D:HOH986 4.6 36.8 1.0
NZ D:LYS622 4.6 33.5 1.0
SG D:CYS270 4.7 40.2 1.0
CA D:CYS572 4.7 37.3 1.0
SG D:CYS508 4.8 34.3 1.0
OG D:SER620 4.9 34.7 1.0
CE D:LYS622 4.9 32.8 1.0
CE1 D:HIS242 5.0 36.5 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 23:10:46 2024

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