Atomistry » Nickel » PDB 6vwz-6z8m » 6ytt
Atomistry »
  Nickel »
    PDB 6vwz-6z8m »
      6ytt »

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

Go back to Nickel Binding Sites List in 6ytt
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

Go back to Nickel Binding Sites List in 6ytt
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

Go back to Nickel Binding Sites List in 6ytt
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

Go back to Nickel Binding Sites List in 6ytt
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

Go back to Nickel Binding Sites List in 6ytt
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

Go back to Nickel Binding Sites List in 6ytt
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: Thu Oct 10 09:01:56 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy