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Nickel in PDB 3i01: Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.

Enzymatic activity of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.

All present enzymatic activity of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.:
1.2.7.4; 1.2.99.2; 2.3.1.169;

Protein crystallography data

The structure of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster., PDB code: 3i01 was solved by Y.Kung, T.I.Doukov, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.96 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.651, 136.870, 140.864, 101.26, 109.11, 104.08
R / Rfree (%) 18.6 / 24.2

Other elements in 3i01:

The structure of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. also contains other interesting chemical elements:

Iron (Fe) 56 atoms
Copper (Cu) 4 atoms
Sodium (Na) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. (pdb code 3i01). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster., PDB code: 3i01:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 3i01

Go back to Nickel Binding Sites List in 3i01
Nickel binding site 1 out of 8 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni800

b:30.2
occ:1.00
 NI A:XCC800 0.0 30.2 1.0
SG A:CYS550 2.2 26.2 1.0
S1 A:XCC800 2.2 22.2 1.0
S4 A:XCC800 2.2 24.7 1.0
FE3 A:XCC800 2.7 22.2 1.0
FE2 A:XCC800 2.8 29.5 1.0
O A:HOH1474 2.9 29.5 1.0
FE1 A:XCC800 3.3 24.3 1.0
CB A:CYS550 3.4 22.4 1.0
FE4 A:XCC800 3.6 24.1 1.0
S3 A:XCC800 3.6 28.8 1.0
O A:HOH676 4.3 20.1 1.0
SG A:CYS317 4.3 25.7 1.0
S2 A:XCC800 4.5 20.5 1.0
NZ A:LYS587 4.5 18.4 1.0
CA A:CYS550 4.6 22.2 1.0
SG A:CYS470 4.7 24.5 1.0
OG A:SER585 4.7 14.5 1.0
CA A:GLY469 4.7 22.1 1.0
C A:GLY469 4.8 21.8 1.0
O A:GLY469 4.8 20.0 1.0
NE2 A:HIS283 4.9 20.6 1.0
CA A:GLY499 4.9 20.4 1.0
O A:HOH707 5.0 30.5 1.0

Nickel binding site 2 out of 8 in 3i01

Go back to Nickel Binding Sites List in 3i01
Nickel binding site 2 out of 8 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni800

b:27.7
occ:1.00
 NI B:XCC800 0.0 27.7 1.0
SG B:CYS550 2.1 23.6 1.0
S4 B:XCC800 2.2 20.9 1.0
S1 B:XCC800 2.2 20.1 1.0
FE3 B:XCC800 2.7 20.2 1.0
FE2 B:XCC800 2.9 25.3 1.0
O B:HOH1472 3.0 20.7 1.0
FE1 B:XCC800 3.4 17.4 1.0
FE4 B:XCC800 3.4 21.8 1.0
CB B:CYS550 3.5 17.6 1.0
S3 B:XCC800 3.6 19.3 1.0
O B:HOH690 4.3 16.3 1.0
S2 B:XCC800 4.4 16.5 1.0
SG B:CYS317 4.4 23.0 1.0
SG B:CYS470 4.5 17.3 1.0
NE2 B:HIS283 4.7 17.2 1.0
NZ B:LYS587 4.7 16.6 1.0
OG B:SER585 4.8 15.1 1.0
CA B:CYS550 4.8 18.1 1.0
CA B:GLY469 4.8 20.8 1.0
CA B:GLY499 4.9 19.0 1.0
C B:GLY469 4.9 19.4 1.0

Nickel binding site 3 out of 8 in 3i01

Go back to Nickel Binding Sites List in 3i01
Nickel binding site 3 out of 8 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni800

b:34.4
occ:1.00
 NI C:XCC800 0.0 34.4 1.0
SG C:CYS550 2.1 25.9 1.0
S4 C:XCC800 2.1 25.8 1.0
S1 C:XCC800 2.4 26.4 1.0
FE3 C:XCC800 2.8 28.8 1.0
FE2 C:XCC800 2.8 35.0 1.0
O C:HOH1436 2.9 34.9 1.0
CB C:CYS550 3.2 23.2 1.0
FE1 C:XCC800 3.4 27.9 1.0
FE4 C:XCC800 3.6 27.6 1.0
S3 C:XCC800 3.8 33.0 1.0
SG C:CYS317 4.3 28.2 1.0
O C:HOH693 4.4 21.0 1.0
NZ C:LYS587 4.5 24.2 1.0
CA C:CYS550 4.6 22.4 1.0
S2 C:XCC800 4.6 25.4 1.0
NE2 C:HIS283 4.7 28.0 1.0
SG C:CYS470 4.8 29.1 1.0
OG C:SER585 4.8 15.4 1.0
CA C:GLY469 4.9 24.5 1.0
CE C:LYS587 5.0 23.9 1.0

Nickel binding site 4 out of 8 in 3i01

Go back to Nickel Binding Sites List in 3i01
Nickel binding site 4 out of 8 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni800

b:45.2
occ:1.00
 NI D:XCC800 0.0 45.2 1.0
SG D:CYS550 2.3 33.7 1.0
S1 D:XCC800 2.3 35.3 1.0
S4 D:XCC800 2.3 37.2 1.0
FE3 D:XCC800 2.7 35.2 1.0
FE2 D:XCC800 2.9 41.3 1.0
O D:HOH1443 2.9 41.8 1.0
FE1 D:XCC800 3.4 34.9 1.0
FE4 D:XCC800 3.5 36.6 1.0
CB D:CYS550 3.5 28.8 1.0
S3 D:XCC800 3.6 35.7 1.0
O D:HOH679 4.2 27.6 1.0
SG D:CYS317 4.3 35.0 1.0
S2 D:XCC800 4.4 33.3 1.0
CA D:GLY469 4.5 27.8 1.0
SG D:CYS470 4.6 32.6 1.0
NE2 D:HIS283 4.6 21.4 1.0
C D:GLY469 4.7 28.5 1.0
CA D:CYS550 4.8 27.1 1.0
CA D:GLY499 4.8 26.6 1.0
CE D:LYS587 4.9 33.3 1.0
OG D:SER585 4.9 26.2 1.0
NZ D:LYS587 4.9 32.3 1.0
N D:GLY469 5.0 27.8 1.0

Nickel binding site 5 out of 8 in 3i01

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Nickel binding site 5 out of 8 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni951

b:28.2
occ:1.00
 N M:CYS597 1.8 26.0 1.0
N M:GLY596 2.1 27.0 1.0
SG M:CYS595 2.2 26.0 1.0
SG M:CYS597 2.2 33.0 1.0
C M:GLY596 2.7 25.2 1.0
CA M:CYS597 2.8 27.8 1.0
CA M:GLY596 2.9 25.1 1.0
CU M:CU1950 3.0 43.6 1.0
CB M:CYS597 3.0 29.0 1.0
CB M:CYS595 3.1 26.3 1.0
C M:CYS595 3.1 26.8 1.0
CA M:CYS595 3.4 27.4 1.0
C M:ACT953 3.5 44.5 1.0
C M:CYS597 3.7 28.1 1.0
N M:PHE598 3.7 27.7 1.0
CD1 M:LEU527 3.7 25.1 1.0
N M:CYS595 3.8 27.4 1.0
O M:ACT953 3.8 45.6 1.0
O M:GLY596 3.9 24.8 1.0
O M:CYS595 4.2 27.6 1.0
CH3 M:ACT953 4.4 44.7 1.0
CD2 M:PHE598 4.6 27.2 1.0
O M:CYS597 4.7 28.5 1.0
S3 M:SF4900 4.8 22.5 1.0
CD1 M:PHE229 4.9 30.6 1.0
CE2 M:PHE598 4.9 31.1 1.0
CA M:PHE598 5.0 27.3 1.0
C M:SER594 5.0 28.1 1.0

Nickel binding site 6 out of 8 in 3i01

Go back to Nickel Binding Sites List in 3i01
Nickel binding site 6 out of 8 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ni951

b:29.2
occ:1.00
 N N:CYS597 1.9 24.9 1.0
N N:GLY596 2.1 25.9 1.0
SG N:CYS595 2.3 24.6 1.0
SG N:CYS597 2.3 29.9 1.0
C N:GLY596 2.8 23.9 1.0
CA N:GLY596 2.8 25.1 1.0
CU N:CU1950 2.9 38.1 1.0
CA N:CYS597 3.0 22.9 1.0
CB N:CYS597 3.1 24.6 1.0
C N:CYS595 3.1 26.3 1.0
CB N:CYS595 3.2 25.9 1.0
C N:ACT953 3.5 59.8 1.0
CA N:CYS595 3.5 25.6 1.0
C N:CYS597 3.6 22.2 1.0
N N:PHE598 3.7 21.7 1.0
N N:CYS595 3.7 24.9 1.0
CD1 N:LEU527 3.8 18.7 1.0
O N:GLY596 4.0 25.3 1.0
O N:CYS595 4.2 26.2 1.0
O N:ACT953 4.2 59.8 1.0
CH3 N:ACT953 4.4 59.4 1.0
CD2 N:PHE598 4.6 21.5 1.0
O N:CYS597 4.7 20.9 1.0
CD1 N:PHE229 4.7 31.6 1.0
CE1 N:PHE229 4.8 35.2 1.0
CE2 N:PHE598 4.8 20.8 1.0
S3 N:SF4900 4.8 26.6 1.0
CA N:PHE598 4.9 21.7 1.0
C N:SER594 5.0 25.5 1.0

Nickel binding site 7 out of 8 in 3i01

Go back to Nickel Binding Sites List in 3i01
Nickel binding site 7 out of 8 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ni951

b:76.5
occ:1.00
 N O:CYS597 2.0 66.7 1.0
N O:GLY596 2.6 66.7 1.0
C O:GLY596 2.9 66.5 1.0
CU O:CU1950 2.9 83.0 1.0
SG O:CYS595 2.9 66.7 1.0
CA O:CYS597 2.9 67.0 1.0
SG O:CYS597 3.0 72.5 1.0
CA O:GLY596 3.1 66.8 1.0
CB O:CYS597 3.3 67.0 1.0
C O:CYS597 3.4 65.9 1.0
N O:PHE598 3.5 64.9 1.0
CD1 O:LEU527 3.5 57.9 1.0
C O:CYS595 3.5 66.7 1.0
C O:ACT953 3.7 0.5 1.0
CA O:CYS595 4.0 66.8 1.0
CB O:CYS595 4.0 66.8 1.0
N O:CYS595 4.0 67.0 1.0
O O:GLY596 4.1 66.2 1.0
CH3 O:ACT953 4.2 0.7 1.0
O O:CYS597 4.3 65.8 1.0
O O:CYS595 4.5 66.5 1.0
CD2 O:PHE598 4.5 63.1 1.0
O O:ACT953 4.6 0.5 1.0
CA O:PHE598 4.6 64.2 1.0
S3 O:SF4900 4.8 63.5 1.0
CG O:LEU527 4.8 58.7 1.0
CE1 O:PHE229 4.9 53.7 1.0
CD2 O:LEU527 5.0 57.6 1.0

Nickel binding site 8 out of 8 in 3i01

Go back to Nickel Binding Sites List in 3i01
Nickel binding site 8 out of 8 in the Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ni951

b:39.9
occ:1.00
 N P:CYS597 1.9 37.6 1.0
N P:GLY596 2.2 41.1 1.0
SG P:CYS597 2.3 38.5 1.0
SG P:CYS595 2.4 44.3 1.0
C P:GLY596 2.8 38.0 1.0
CB P:CYS597 2.9 38.3 1.0
CA P:CYS597 2.9 37.3 1.0
CU P:CU1950 3.0 55.8 1.0
CA P:GLY596 3.0 38.4 1.0
CB P:CYS595 3.1 43.3 1.0
C P:CYS595 3.2 42.5 1.0
C P:ACT953 3.5 54.4 1.0
CA P:CYS595 3.5 43.5 1.0
N P:PHE598 3.7 37.5 1.0
C P:CYS597 3.7 37.3 1.0
CD1 P:LEU527 3.8 39.5 1.0
N P:CYS595 3.8 44.2 1.0
O P:GLY596 4.0 36.2 1.0
O P:ACT953 4.2 54.4 1.0
CH3 P:ACT953 4.3 53.4 1.0
O P:CYS595 4.3 43.7 1.0
CD1 P:PHE229 4.4 35.2 1.0
CE1 P:PHE229 4.5 34.4 1.0
CD2 P:PHE598 4.5 33.3 1.0
O P:CYS597 4.7 36.4 1.0
S3 P:SF4900 4.7 40.7 1.0
CA P:PHE598 4.9 37.3 1.0
CE2 P:PHE598 4.9 34.9 1.0

Reference:

Y.Kung, T.I.Doukov, J.Seravalli, S.W.Ragsdale, C.L.Drennan. Crystallographic Snapshots of Cyanide- and Water-Bound C-Clusters From Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase. Biochemistry V. 48 7432 2009.
ISSN: ISSN 0006-2960
PubMed: 19583207
DOI: 10.1021/BI900574H
Page generated: Wed Oct 9 17:22:59 2024

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