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Nickel in PDB 6x5k: Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster

Enzymatic activity of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster

All present enzymatic activity of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster:
1.2.7.4; 2.3.1.169;

Protein crystallography data

The structure of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster, PDB code: 6x5k was solved by S.E.Cohen, E.C.Wittenborn, R.Hendrickson, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.63 / 2.47
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.729, 137.383, 141.867, 101.82, 109.08, 103.66
R / Rfree (%) 20.3 / 23.4

Other elements in 6x5k:

The structure of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 56 atoms

Nickel Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Nickel atom in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster (pdb code 6x5k). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster, PDB code: 6x5k:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 12 in 6x5k

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Nickel binding site 1 out of 12 in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster


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 Codh/Acs with Carbon Monoxide Bound to the A- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni703

b:69.0
occ:1.00
 NI A:XCC703 0.0 69.0 1.0
SG A:CYS550 2.2 50.6 0.7
O A:HOH882 2.3 37.4 1.0
S4 A:XCC703 2.3 61.0 1.0
S1 A:XCC703 2.3 56.1 1.0
FE3 A:XCC703 2.7 63.8 1.0
FE2 A:XCC703 2.9 51.5 1.0
CB A:CYS550 3.5 44.9 0.7
CB A:CYS550 3.5 45.0 0.3
FE1 A:XCC703 3.5 47.5 1.0
S3 A:XCC703 3.8 44.0 1.0
FE4 A:XCC703 3.9 55.8 1.0
SG A:CYS550 4.1 45.6 0.3
SG A:CYS470 4.4 39.3 1.0
OG A:SER585 4.4 29.4 1.0
NE2 A:HIS283 4.5 50.6 1.0
SG A:CYS317 4.5 44.3 1.0
O A:HOH857 4.5 40.9 1.0
S2 A:XCC703 4.6 52.5 1.0
CE A:LYS587 4.7 34.0 1.0
NZ A:LYS587 4.7 31.3 1.0
CA A:CYS550 4.8 41.8 0.3
CA A:CYS550 4.8 41.7 0.7
O A:GLY469 4.8 40.5 1.0
CB A:LYS587 5.0 28.1 1.0

Nickel binding site 2 out of 12 in 6x5k

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Nickel binding site 2 out of 12 in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster


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 Codh/Acs with Carbon Monoxide Bound to the A- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni702

b:64.2
occ:1.00
 NI B:XCC702 0.0 64.2 1.0
SG B:CYS550 2.2 49.5 0.7
S1 B:XCC702 2.3 43.1 1.0
S4 B:XCC702 2.3 82.8 1.0
O B:HOH876 2.4 31.2 1.0
FE3 B:XCC702 2.7 71.0 1.0
FE2 B:XCC702 3.0 53.3 1.0
FE1 B:XCC702 3.5 48.0 1.0
CB B:CYS550 3.6 43.7 0.7
CB B:CYS550 3.6 44.1 0.3
S3 B:XCC702 3.8 41.4 1.0
FE4 B:XCC702 4.1 54.9 1.0
SG B:CYS550 4.2 44.5 0.3
SG B:CYS470 4.4 50.5 1.0
S2 B:XCC702 4.5 58.2 1.0
OG B:SER585 4.5 34.0 1.0
SG B:CYS317 4.5 37.2 1.0
NZ B:LYS587 4.7 33.0 1.0
NE2 B:HIS283 4.7 48.8 1.0
CE B:LYS587 4.7 36.6 1.0
O B:GLY469 4.8 46.4 1.0
CA B:CYS550 4.8 41.3 0.3
CA B:CYS550 4.8 41.3 0.7
CB B:LYS587 5.0 27.7 1.0

Nickel binding site 3 out of 12 in 6x5k

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Nickel binding site 3 out of 12 in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni703

b:73.2
occ:1.00
 NI C:XCC703 0.0 73.2 1.0
SG C:CYS550 2.1 58.2 0.7
S1 C:XCC703 2.3 0.2 1.0
S4 C:XCC703 2.3 56.1 1.0
O C:HOH844 2.4 29.0 1.0
FE3 C:XCC703 2.9 70.2 1.0
FE2 C:XCC703 2.9 58.3 1.0
CB C:CYS550 3.6 53.0 0.7
FE1 C:XCC703 3.6 64.1 1.0
CB C:CYS550 3.7 53.0 0.3
S3 C:XCC703 3.9 45.6 1.0
O C:HOH840 3.9 42.6 1.0
FE4 C:XCC703 4.0 58.3 1.0
SG C:CYS470 4.3 44.8 1.0
SG C:CYS317 4.4 50.5 1.0
OG C:SER585 4.4 38.8 1.0
SG C:CYS550 4.6 53.6 0.3
S2 C:XCC703 4.6 64.8 1.0
CE C:LYS587 4.7 45.4 1.0
NE2 C:HIS283 4.7 55.9 1.0
O C:GLY469 4.7 60.1 1.0
NZ C:LYS587 4.8 44.9 1.0
CA C:CYS550 4.8 49.7 0.3
CA C:CYS550 4.9 49.9 0.7
CB C:LYS587 4.9 38.1 1.0

Nickel binding site 4 out of 12 in 6x5k

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Nickel binding site 4 out of 12 in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni702

b:84.2
occ:1.00
 NI D:XCC702 0.0 84.2 1.0
SG D:CYS550 2.2 75.0 1.0
S1 D:XCC702 2.3 50.8 1.0
S4 D:XCC702 2.3 74.1 1.0
FE3 D:XCC702 2.7 69.3 1.0
FE2 D:XCC702 3.1 57.4 1.0
CB D:CYS550 3.7 61.7 1.0
FE1 D:XCC702 3.7 64.4 1.0
FE4 D:XCC702 4.1 58.3 1.0
S3 D:XCC702 4.3 58.8 1.0
SG D:CYS470 4.3 54.5 1.0
OG D:SER585 4.4 49.3 1.0
O D:GLY469 4.5 60.7 1.0
SG D:CYS317 4.6 54.5 1.0
S2 D:XCC702 4.7 69.1 1.0
NE2 D:HIS283 4.8 54.2 1.0
CE D:LYS587 4.9 48.2 1.0
CA D:CYS550 4.9 51.1 1.0
CB D:LYS587 4.9 43.2 1.0
C D:GLY469 4.9 60.1 1.0

Nickel binding site 5 out of 12 in 6x5k

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Nickel binding site 5 out of 12 in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni802

b:48.4
occ:1.00
 C M:CMO804 1.7 44.1 1.0
SG M:CYS597 2.3 37.1 1.0
SG M:CYS595 2.3 38.5 1.0
SG M:CYS509 2.3 34.6 1.0
NI M:NI803 2.7 31.4 1.0
O M:CMO804 2.8 43.3 1.0
CB M:CYS509 3.2 33.1 1.0
CB M:CYS595 3.4 37.5 1.0
CB M:CYS597 3.4 28.1 1.0
FE4 M:SF4801 3.9 32.3 1.0
S3 M:SF4801 4.0 28.6 1.0
N M:CYS597 4.0 29.4 1.0
N M:GLY596 4.3 32.8 1.0
CA M:CYS597 4.4 27.9 1.0
CA M:CYS509 4.6 33.6 1.0
CA M:CYS595 4.6 36.8 1.0
CD1 M:ILE146 4.8 44.6 1.0
C M:CYS595 4.8 35.0 1.0
C M:GLY596 5.0 33.4 1.0

Nickel binding site 6 out of 12 in 6x5k

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Nickel binding site 6 out of 12 in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni803

b:31.4
occ:1.00
 N M:CYS597 1.9 29.4 1.0
N M:GLY596 2.0 32.8 1.0
SG M:CYS595 2.2 38.5 1.0
SG M:CYS597 2.4 37.1 1.0
NI M:NI802 2.7 48.4 1.0
C M:GLY596 2.7 33.4 1.0
CA M:GLY596 2.9 31.6 1.0
CA M:CYS597 2.9 27.9 1.0
CB M:CYS597 3.0 28.1 1.0
C M:CYS595 3.1 35.0 1.0
CB M:CYS595 3.1 37.5 1.0
CA M:CYS595 3.4 36.8 1.0
C M:CMO804 3.5 44.1 1.0
N M:CYS595 3.7 37.6 1.0
C M:CYS597 3.7 31.5 1.0
N M:PHE598 3.7 30.9 1.0
CD1 M:LEU527 3.8 34.9 1.0
O M:GLY596 3.9 38.9 1.0
O M:CYS595 4.2 34.7 1.0
O M:CMO804 4.5 43.3 1.0
CD2 M:PHE598 4.7 38.5 1.0
S3 M:SF4801 4.7 28.6 1.0
O M:CYS597 4.8 33.5 1.0
SG M:CYS509 4.9 34.6 1.0
C M:SER594 4.9 38.2 1.0
CD1 M:PHE229 4.9 40.6 1.0
CA M:PHE598 5.0 34.2 1.0

Nickel binding site 7 out of 12 in 6x5k

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Nickel binding site 7 out of 12 in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ni802

b:44.0
occ:1.00
 C N:CMO804 1.6 42.7 1.0
SG N:CYS597 2.3 30.3 1.0
SG N:CYS595 2.3 35.8 1.0
SG N:CYS509 2.4 38.5 1.0
NI N:NI803 2.7 31.8 1.0
O N:CMO804 2.8 40.6 1.0
CB N:CYS509 3.3 35.9 1.0
CB N:CYS595 3.4 38.2 1.0
CB N:CYS597 3.4 30.0 1.0
FE4 N:SF4801 3.9 32.3 1.0
N N:CYS597 4.0 28.4 1.0
S3 N:SF4801 4.0 32.6 1.0
N N:GLY596 4.2 30.2 1.0
CA N:CYS597 4.4 31.2 1.0
CA N:CYS509 4.6 35.6 1.0
CA N:CYS595 4.6 39.7 1.0
CD1 N:ILE146 4.6 41.4 1.0
C N:CYS595 4.8 35.6 1.0
C N:GLY596 4.9 29.4 1.0

Nickel binding site 8 out of 12 in 6x5k

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Nickel binding site 8 out of 12 in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ni803

b:31.8
occ:1.00
 N N:CYS597 1.9 28.4 1.0
N N:GLY596 2.0 30.2 1.0
SG N:CYS595 2.2 35.8 1.0
SG N:CYS597 2.4 30.3 1.0
C N:GLY596 2.7 29.4 1.0
NI N:NI802 2.7 44.0 1.0
CA N:GLY596 2.8 27.7 1.0
CA N:CYS597 2.9 31.2 1.0
CB N:CYS597 3.0 30.0 1.0
C N:CYS595 3.1 35.6 1.0
CB N:CYS595 3.1 38.2 1.0
CA N:CYS595 3.4 39.7 1.0
C N:CMO804 3.5 42.7 1.0
N N:CYS595 3.6 42.0 1.0
C N:CYS597 3.7 33.9 1.0
N N:PHE598 3.7 33.9 1.0
CD1 N:LEU527 3.8 25.8 1.0
O N:GLY596 3.9 29.4 1.0
O N:CYS595 4.2 38.4 1.0
O N:CMO804 4.4 40.6 1.0
CD2 N:PHE598 4.6 31.4 1.0
S3 N:SF4801 4.7 32.6 1.0
O N:CYS597 4.7 32.1 1.0
C N:SER594 4.9 41.5 1.0
SG N:CYS509 4.9 38.5 1.0
CE2 N:PHE598 4.9 30.1 1.0
CA N:PHE598 5.0 32.9 1.0
CD1 N:PHE229 5.0 41.0 1.0

Nickel binding site 9 out of 12 in 6x5k

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Nickel binding site 9 out of 12 in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ni901

b:75.7
occ:1.00
 SG O:CYS595 2.3 99.5 1.0
SG O:CYS597 2.3 80.4 1.0
SG O:CYS509 2.4 82.4 1.0
NI O:NI902 2.8 90.3 1.0
CB O:CYS509 3.3 82.1 1.0
CB O:CYS595 3.4 98.3 1.0
CB O:CYS597 3.5 81.1 1.0
FE4 O:SF4900 4.0 88.2 1.0
N O:CYS597 4.1 87.2 1.0
S3 O:SF4900 4.1 63.7 1.0
N O:GLY596 4.2 93.1 1.0
CA O:CYS597 4.4 82.3 1.0
CA O:CYS595 4.6 97.2 1.0
CG1 O:VAL149 4.6 69.8 1.0
CA O:CYS509 4.6 81.8 1.0
C O:CYS595 4.7 97.4 1.0
C O:GLY596 4.9 89.1 1.0
CD1 O:ILE146 4.9 59.5 1.0
CD1 O:PHE229 4.9 70.8 1.0

Nickel binding site 10 out of 12 in 6x5k

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Nickel binding site 10 out of 12 in the Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of Codh/Acs with Carbon Monoxide Bound to the A- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ni902

b:90.3
occ:1.00
 N O:CYS597 1.9 87.2 1.0
N O:GLY596 2.1 93.1 1.0
SG O:CYS595 2.1 99.5 1.0
SG O:CYS597 2.4 80.4 1.0
C O:GLY596 2.8 89.1 1.0
NI O:NI901 2.8 75.7 1.0
CA O:GLY596 2.9 92.0 1.0
CA O:CYS597 2.9 82.3 1.0
CB O:CYS597 3.0 81.1 1.0
C O:CYS595 3.1 97.4 1.0
CB O:CYS595 3.2 98.3 1.0
CA O:CYS595 3.5 97.2 1.0
N O:CYS595 3.6 96.7 1.0
C O:CYS597 3.7 80.3 1.0
N O:PHE598 3.7 78.7 1.0
CD1 O:LEU527 3.8 77.2 1.0
O O:GLY596 3.9 88.4 1.0
O O:CYS595 4.2 97.5 1.0
CD2 O:PHE598 4.6 81.2 1.0
S3 O:SF4900 4.7 63.7 1.0
O O:CYS597 4.7 79.8 1.0
CD1 O:PHE229 4.7 70.8 1.0
C O:SER594 4.9 0.7 1.0
CE1 O:PHE229 4.9 71.1 1.0
CA O:PHE598 5.0 78.0 1.0
SG O:CYS509 5.0 82.4 1.0

Reference:

S.E.Cohen, M.Can, E.C.Wittenborn, R.A.Hendrickson, S.W.Ragsdale, C.L.Drennan. Crystallographic Characterization of the Carbonylated A-Cluster in Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase Acs Catalysis V. 10 9741 2020.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.0C03033
Page generated: Thu Oct 10 08:58:39 2024

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