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Nickel in PDB 6ytt: Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution

Enzymatic activity of Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution

All present enzymatic activity of Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution:
1.2.99.2; 2.3.1.169;

Protein crystallography data

The structure of Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution, PDB code: 6ytt 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) 49.15 / 3.01
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 298.943, 298.943, 128.895, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22

Other elements in 6ytt:

The structure of Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Iron (Fe) 28 atoms
Sodium (Na) 6 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution (pdb code 6ytt). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution, PDB code: 6ytt:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 6ytt

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Nickel binding site 1 out of 6 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni807

b:95.0
occ:1.00
N A:CYS576 2.0 1.0 1.0
N A:GLY575 2.1 0.7 1.0
SG A:CYS574 2.2 0.5 1.0
SG A:CYS576 2.6 95.0 1.0
CB A:CYS574 2.9 98.8 1.0
C A:GLY575 2.9 96.8 1.0
NI A:NI808 2.9 0.1 1.0
CA A:GLY575 3.0 95.5 1.0
CA A:CYS576 3.0 82.3 1.0
C A:CYS574 3.1 93.2 1.0
CB A:CYS576 3.3 84.2 1.0
CA A:CYS574 3.4 89.4 1.0
C A:CYS576 3.7 84.5 1.0
N A:PHE577 3.7 78.6 1.0
CD1 A:LEU506 3.8 1.0 1.0
N A:CYS574 3.9 86.9 1.0
O A:GLY575 4.1 97.7 1.0
O A:CYS574 4.3 96.7 1.0
CZ A:PHE491 4.3 91.8 1.0
CD2 A:PHE577 4.5 91.5 1.0
S1 A:SF4804 4.5 0.1 1.0
CE2 A:PHE491 4.6 95.6 1.0
SG A:CYS488 4.6 0.1 1.0
O A:CYS576 4.6 0.2 1.0
CE2 A:PHE577 4.8 99.7 1.0
CA A:PHE577 4.9 88.2 1.0

Nickel binding site 2 out of 6 in 6ytt

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Nickel binding site 2 out of 6 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni808

b:0.1
occ:1.00
SG A:CYS574 2.2 0.5 1.0
FE4 A:SF4804 2.2 0.5 1.0
S1 A:SF4804 2.4 0.1 1.0
SG A:CYS576 2.6 95.0 1.0
SG A:CYS488 2.7 0.1 1.0
NI A:NI807 2.9 95.0 1.0
CB A:CYS488 3.2 0.2 1.0
CB A:CYS574 3.2 98.8 1.0
S3 A:SF4804 3.8 0.2 1.0
FE2 A:SF4804 3.8 0.9 1.0
FE3 A:SF4804 4.1 0.8 1.0
S2 A:SF4804 4.2 0.7 1.0
CB A:CYS576 4.3 84.2 1.0
CD1 A:LEU506 4.3 1.0 1.0
N A:GLY575 4.6 0.7 1.0
N A:CYS576 4.6 1.0 1.0
CZ A:PHE491 4.6 91.8 1.0
CA A:CYS574 4.6 89.4 1.0
NE2 A:HIS495 4.6 0.9 1.0
CA A:CYS488 4.7 0.6 1.0
CD2 A:HIS495 4.7 99.0 1.0
FE1 A:SF4804 4.8 0.2 1.0
CB A:CYS507 5.0 84.3 1.0
CA A:CYS576 5.0 82.3 1.0

Nickel binding site 3 out of 6 in 6ytt

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Nickel binding site 3 out of 6 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni709

b:0.5
occ:1.00
NI B:XCC709 0.0 0.5 1.0
S1 B:XCC709 2.3 0.3 1.0
FE2 B:XCC709 2.6 0.6 1.0
S4 B:XCC709 2.7 72.9 1.0
SG B:CYS523 3.0 92.2 1.0
FE3 B:XCC709 3.4 0.1 1.0
S3 B:XCC709 3.6 0.3 1.0
CB B:CYS523 3.6 43.8 1.0
FE4 B:XCC709 3.8 0.8 1.0
FE1 B:XCC709 4.1 0.4 1.0
S2 B:XCC709 4.2 96.5 1.0
OG B:SER558 4.4 52.5 1.0
CE B:LYS560 4.7 41.7 1.0
NZ B:LYS560 4.8 49.7 1.0
NE2 B:HIS259 4.8 63.8 1.0
SG B:CYS295 4.9 72.4 1.0
CB B:LYS560 5.0 59.2 1.0
SG B:CYS451 5.0 63.9 1.0
CD1 B:ILE564 5.0 43.0 1.0

Nickel binding site 4 out of 6 in 6ytt

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Nickel binding site 4 out of 6 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-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/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni1005

b:0.8
occ:1.00
NI C:XCC1005 0.0 0.8 1.0
S1 C:XCC1005 2.3 0.0 1.0
FE2 C:XCC1005 2.5 0.4 1.0
S4 C:XCC1005 2.6 0.7 1.0
SG C:CYS523 3.0 0.7 1.0
CB C:CYS523 3.2 80.9 1.0
S3 C:XCC1005 3.4 0.2 1.0
FE3 C:XCC1005 3.4 1.0 1.0
SG C:CYS295 3.5 97.8 1.0
FE4 C:XCC1005 3.8 0.8 1.0
FE1 C:XCC1005 3.9 0.6 1.0
NE2 C:HIS259 4.1 64.0 1.0
S2 C:XCC1005 4.1 0.9 1.0
CA C:CYS523 4.4 67.8 1.0
CA C:GLY480 4.5 78.6 1.0
N C:CYS523 4.5 64.2 1.0
CD2 C:HIS259 4.8 74.4 1.0
N C:CYS481 4.9 54.0 1.0
CB C:CYS295 5.0 82.0 1.0

Nickel binding site 5 out of 6 in 6ytt

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Nickel binding site 5 out of 6 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1003

b:89.1
occ:1.00
SG D:CYS574 2.1 0.6 1.0
SG D:CYS576 2.2 0.9 1.0
SG D:CYS488 2.6 0.7 1.0
S1 D:SF41002 2.7 0.3 1.0
NI D:NI1004 2.7 85.0 1.0
FE4 D:SF41002 2.7 0.6 1.0
CB D:CYS574 3.3 0.6 1.0
CB D:CYS576 3.7 0.1 1.0
N D:CYS576 3.9 0.2 1.0
CB D:CYS488 3.9 0.4 1.0
CD1 D:LEU506 4.1 0.9 1.0
N D:GLY575 4.2 1.0 1.0
FE3 D:SF41002 4.3 0.7 1.0
CA D:CYS576 4.3 0.9 1.0
S2 D:SF41002 4.4 0.5 1.0
FE2 D:SF41002 4.4 0.2 1.0
CA D:CYS574 4.5 0.2 1.0
S3 D:SF41002 4.6 0.6 1.0
CZ D:PHE491 4.8 0.1 1.0
CG D:LEU506 4.8 0.4 1.0
CB D:CYS507 4.9 0.1 1.0
C D:CYS576 4.9 0.9 1.0
C D:CYS574 4.9 0.2 1.0
N D:CYS574 5.0 0.0 1.0
C D:GLY575 5.0 0.6 1.0

Nickel binding site 6 out of 6 in 6ytt

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Nickel binding site 6 out of 6 in the Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1004

b:85.0
occ:1.00
N D:CYS576 1.9 0.2 1.0
N D:GLY575 2.0 1.0 1.0
SG D:CYS574 2.5 0.6 1.0
C D:GLY575 2.6 0.6 1.0
NI D:NI1003 2.7 89.1 1.0
CA D:GLY575 2.7 0.5 1.0
CA D:CYS576 3.0 0.9 1.0
SG D:CYS576 3.0 0.9 1.0
C D:CYS574 3.1 0.2 1.0
CB D:CYS574 3.1 0.6 1.0
N D:PHE577 3.4 93.8 1.0
CB D:CYS576 3.4 0.1 1.0
CD1 D:LEU506 3.5 0.9 1.0
C D:CYS576 3.5 0.9 1.0
CA D:CYS574 3.5 0.2 1.0
O D:GLY575 3.8 0.1 1.0
N D:CYS574 3.9 0.0 1.0
CD2 D:PHE577 4.2 90.5 1.0
O D:CYS574 4.2 0.9 1.0
CA D:PHE577 4.5 0.8 1.0
SG D:CYS488 4.5 0.7 1.0
O D:CYS576 4.5 0.0 1.0
CG D:PHE577 4.6 97.5 1.0
CZ D:PHE491 4.6 0.1 1.0
CE2 D:PHE577 4.7 0.5 1.0
CB D:PHE577 4.8 96.8 1.0
S1 D:SF41002 4.8 0.3 1.0
CG D:LEU506 4.8 0.4 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: Wed Dec 16 01:57:19 2020

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