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Nickel in PDB 6yu9: Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution

Enzymatic activity of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution

All present enzymatic activity of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution:
1.2.99.2;

Protein crystallography data

The structure of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution, PDB code: 6yu9 was solved by T.Wagner, O.N.Lemaire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.75 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.531, 109.446, 129.280, 90.00, 112.55, 90.00
R / Rfree (%) 15.8 / 20.3

Other elements in 6yu9:

The structure of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution also contains other interesting chemical elements:

Iron (Fe) 40 atoms
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution (pdb code 6yu9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution, PDB code: 6yu9:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 6yu9

Go back to Nickel Binding Sites List in 6yu9
Nickel binding site 1 out of 4 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni706

b:40.8
occ:1.00
 NI A:XCC706 0.0 40.8 1.0
S1 A:XCC706 2.2 28.2 1.0
S4 A:XCC706 2.3 22.9 1.0
SG A:CYS523 2.5 22.5 1.0
O A:HOH995 2.6 43.4 1.0
FE3 A:XCC706 2.7 25.9 1.0
FE2 A:XCC706 2.8 27.6 1.0
FE1 A:XCC706 3.0 22.2 1.0
S3 A:XCC706 3.4 23.3 1.0
FE4 A:XCC706 3.4 25.4 1.0
CB A:CYS523 3.8 17.3 1.0
S2 A:XCC706 4.1 24.7 1.0
SG A:CYS295 4.2 24.9 1.0
NE2 A:HIS259 4.5 23.5 1.0
NZ A:LYS560 4.6 14.9 1.0
SG A:CYS451 4.6 14.2 1.0
O A:HOH860 4.8 25.6 1.0
CE A:LYS560 4.9 14.4 1.0
OG A:SER558 4.9 15.4 1.0
SG A:CYS333 5.0 12.7 1.0
N A:CYS451 5.0 11.3 1.0

Nickel binding site 2 out of 4 in 6yu9

Go back to Nickel Binding Sites List in 6yu9
Nickel binding site 2 out of 4 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni703

b:39.1
occ:1.00
 NI B:XCC703 0.0 39.1 1.0
SG B:CYS523 2.2 36.2 1.0
S1 B:XCC703 2.3 23.4 1.0
S4 B:XCC703 2.5 18.8 1.0
FE2 B:XCC703 2.7 30.1 1.0
FE3 B:XCC703 2.8 19.4 1.0
FE1 B:XCC703 3.4 23.5 1.0
CB B:CYS523 3.5 24.5 1.0
FE4 B:XCC703 3.6 22.1 1.0
S3 B:XCC703 3.6 23.5 1.0
SG B:CYS295 4.2 21.7 1.0
O B:HOH934 4.3 21.4 1.0
S2 B:XCC703 4.5 22.1 1.0
NE2 B:HIS259 4.6 31.3 1.0
NZ B:LYS560 4.6 20.8 1.0
SG B:CYS451 4.8 17.2 1.0
CA B:CYS523 4.8 22.6 1.0

Nickel binding site 3 out of 4 in 6yu9

Go back to Nickel Binding Sites List in 6yu9
Nickel binding site 3 out of 4 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni703

b:45.7
occ:1.00
 NI C:XCC703 0.0 45.7 1.0
SG C:CYS523 2.2 46.2 1.0
S4 C:XCC703 2.3 26.0 1.0
S1 C:XCC703 2.5 34.8 1.0
FE2 C:XCC703 2.7 35.4 1.0
FE3 C:XCC703 3.0 30.7 1.0
FE1 C:XCC703 3.2 28.1 1.0
S3 C:XCC703 3.4 31.0 1.0
FE4 C:XCC703 3.4 32.6 1.0
CB C:CYS523 3.5 34.5 1.0
SG C:CYS295 4.2 35.9 1.0
NZ C:LYS560 4.4 25.1 1.0
S2 C:XCC703 4.5 29.5 1.0
NE2 C:HIS259 4.5 44.6 1.0
O C:HOH888 4.6 21.8 1.0
CE C:LYS560 4.6 27.4 1.0
CA C:CYS523 4.9 31.1 1.0
O C:HOH930 4.9 32.3 1.0
SG C:CYS333 4.9 31.0 1.0
OG C:SER558 4.9 23.3 1.0

Nickel binding site 4 out of 4 in 6yu9

Go back to Nickel Binding Sites List in 6yu9
Nickel binding site 4 out of 4 in the Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Co-Dehydrogenase Homodimer From Clostridium Autoethanogenum at 1.90-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni703

b:33.8
occ:1.00
 NI D:XCC703 0.0 33.8 1.0
S1 D:XCC703 2.3 22.7 1.0
S4 D:XCC703 2.4 19.1 1.0
SG D:CYS523 2.4 27.4 1.0
FE3 D:XCC703 2.7 21.1 1.0
FE2 D:XCC703 2.8 29.8 1.0
FE1 D:XCC703 3.2 20.9 1.0
FE4 D:XCC703 3.2 19.8 1.0
S3 D:XCC703 3.4 21.6 1.0
CB D:CYS523 3.7 20.1 1.0
SG D:CYS295 4.3 19.6 1.0
S2 D:XCC703 4.4 17.1 1.0
O D:HOH954 4.5 5.8 1.0
NE2 D:HIS259 4.5 23.9 1.0
SG D:CYS451 4.7 22.7 1.0
NZ D:LYS560 4.9 17.9 1.0
CE D:LYS560 4.9 15.9 1.0
OG D:SER558 5.0 24.2 1.0

Reference:

O.N.Lemaire, T.Wagner. Gas Channel Rerouting in A Primordial Enzyme: Structural Insights of the Carbon-Monoxide Dehydrogenase/Acetyl-Coa Synthase Complex From the Acetogen Clostridium Autoethanogenum. Biochim Biophys Acta V.1862 48330 2020BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 33080205
DOI: 10.1016/J.BBABIO.2020.148330
Page generated: Thu Oct 10 09:01:59 2024

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