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Copper 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:

Nickel (Ni) 8 atoms
Iron (Fe) 56 atoms
Sodium (Na) 4 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 4 binding sites of Copper 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 Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 3i01

Go back to Copper Binding Sites List in 3i01
Copper binding site 1 out of 4 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 Copper with other atoms in the Cu 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
M:Cu950

b:43.6
occ:1.00
 SG M:CYS595 2.3 26.0 1.0
SG M:CYS597 2.3 33.0 1.0
SG M:CYS509 2.3 24.6 1.0
C M:ACT953 2.7 44.5 1.0
FE4 M:SF4900 2.9 25.2 1.0
NI M:NI951 3.0 28.2 1.0
S3 M:SF4900 3.0 22.5 1.0
CB M:CYS509 3.2 18.6 1.0
O M:ACT953 3.4 45.6 1.0
CB M:CYS595 3.5 26.3 1.0
CB M:CYS597 3.7 29.0 1.0
CH3 M:ACT953 3.8 44.7 1.0
CD1 M:ILE146 4.1 21.5 1.0
N M:CYS597 4.4 26.0 1.0
CD1 M:LEU527 4.5 25.1 1.0
S2 M:SF4900 4.6 24.8 1.0
CA M:CYS509 4.6 22.2 1.0
CA M:CYS597 4.6 27.8 1.0
N M:GLY596 4.7 27.0 1.0
FE1 M:SF4900 4.7 24.5 1.0
FE2 M:SF4900 4.7 28.3 1.0
CA M:CYS595 4.8 27.4 1.0
S1 M:SF4900 4.8 26.4 1.0
CD2 M:HIS516 4.9 21.5 1.0

Copper binding site 2 out of 4 in 3i01

Go back to Copper Binding Sites List in 3i01
Copper binding site 2 out of 4 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 Copper with other atoms in the Cu 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
N:Cu950

b:38.1
occ:1.00
 SG N:CYS509 2.2 24.9 1.0
SG N:CYS595 2.3 24.6 1.0
SG N:CYS597 2.3 29.9 1.0
FE4 N:SF4900 2.9 26.3 1.0
NI N:NI951 2.9 29.2 1.0
C N:ACT953 3.0 59.8 1.0
S3 N:SF4900 3.0 26.6 1.0
CB N:CYS509 3.2 22.6 1.0
O N:ACT953 3.3 59.8 1.0
CB N:CYS595 3.5 25.9 1.0
CH3 N:ACT953 3.8 59.4 1.0
CB N:CYS597 3.8 24.6 1.0
CD1 N:ILE146 3.9 37.2 1.0
N N:CYS597 4.4 24.9 1.0
S2 N:SF4900 4.5 28.1 1.0
CA N:CYS509 4.6 25.4 1.0
FE2 N:SF4900 4.7 27.4 1.0
N N:GLY596 4.7 25.9 1.0
FE1 N:SF4900 4.7 25.3 1.0
CA N:CYS597 4.7 22.9 1.0
S1 N:SF4900 4.7 26.7 1.0
CD1 N:LEU527 4.7 18.7 1.0
CA N:CYS595 4.8 25.6 1.0

Copper binding site 3 out of 4 in 3i01

Go back to Copper Binding Sites List in 3i01
Copper binding site 3 out of 4 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 Copper with other atoms in the Cu 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
O:Cu950

b:83.0
occ:1.00
 SG O:CYS509 2.2 54.1 1.0
SG O:CYS595 2.8 66.7 1.0
C O:ACT953 2.9 0.5 1.0
SG O:CYS597 2.9 72.5 1.0
NI O:NI951 2.9 76.5 1.0
S3 O:SF4900 3.2 63.5 1.0
O O:ACT953 3.2 0.5 1.0
FE4 O:SF4900 3.2 65.4 1.0
CB O:CYS509 3.3 56.8 1.0
CH3 O:ACT953 3.5 0.7 1.0
CB O:CYS597 4.1 67.0 1.0
CD1 O:LEU527 4.2 57.9 1.0
CD1 O:ILE146 4.3 49.8 1.0
CB O:CYS595 4.4 66.8 1.0
N O:CYS597 4.4 66.7 1.0
CA O:CYS509 4.7 56.8 1.0
CA O:CYS597 4.8 67.0 1.0
FE2 O:SF4900 4.9 65.6 1.0
CB O:CYS528 4.9 60.5 1.0
FE1 O:SF4900 5.0 67.5 1.0
S1 O:SF4900 5.0 61.3 1.0

Copper binding site 4 out of 4 in 3i01

Go back to Copper Binding Sites List in 3i01
Copper binding site 4 out of 4 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 Copper with other atoms in the Cu 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
P:Cu950

b:55.8
occ:1.00
 SG P:CYS597 2.2 38.5 1.0
SG P:CYS509 2.2 40.1 1.0
SG P:CYS595 2.5 44.3 1.0
C P:ACT953 2.7 54.4 1.0
NI P:NI951 3.0 39.9 1.0
FE4 P:SF4900 3.0 40.9 1.0
S3 P:SF4900 3.0 40.7 1.0
CB P:CYS509 3.2 37.1 1.0
CH3 P:ACT953 3.4 53.4 1.0
CB P:CYS597 3.5 38.3 1.0
O P:ACT953 3.5 54.4 1.0
CB P:CYS595 3.6 43.3 1.0
N P:CYS597 4.5 37.6 1.0
CD1 P:LEU527 4.5 39.5 1.0
CD1 P:ILE146 4.5 32.4 1.0
CA P:CYS509 4.5 38.5 1.0
CA P:CYS597 4.6 37.3 1.0
S2 P:SF4900 4.7 41.0 1.0
FE2 P:SF4900 4.7 40.7 1.0
FE1 P:SF4900 4.8 40.8 1.0
N P:GLY596 4.8 41.1 1.0
S1 P:SF4900 4.9 46.2 1.0
CA P:CYS595 4.9 43.5 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 Jul 31 01:04:37 2024

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