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Copper in PDB 3i04: Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster

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

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

Protein crystallography data

The structure of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster, PDB code: 3i04 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) 48.39 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.830, 136.768, 141.611, 101.23, 109.18, 103.87
R / Rfree (%) 17.2 / 22.1

Other elements in 3i04:

The structure of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-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 Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster (pdb code 3i04). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster, PDB code: 3i04:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 3i04

Go back to Copper Binding Sites List in 3i04
Copper binding site 1 out of 4 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-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 Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cu950

b:35.4
occ:1.00
SG M:CYS509 2.2 23.2 1.0
SG M:CYS597 2.3 23.4 1.0
SG M:CYS595 2.3 23.7 1.0
FE4 M:SF4900 2.9 22.7 1.0
S3 M:SF4900 2.9 22.7 1.0
C M:ACT953 2.9 56.3 1.0
NI M:NI951 3.0 24.4 1.0
CB M:CYS509 3.2 18.4 1.0
O M:ACT953 3.5 56.7 1.0
CB M:CYS595 3.6 23.7 1.0
CB M:CYS597 3.7 23.7 1.0
CD1 M:ILE146 3.9 25.3 1.0
CH3 M:ACT953 4.0 56.0 1.0
N M:CYS597 4.3 21.9 1.0
S2 M:SF4900 4.5 20.0 1.0
FE1 M:SF4900 4.5 21.8 1.0
CD1 M:LEU527 4.6 28.1 1.0
CA M:CYS509 4.6 21.0 1.0
N M:GLY596 4.6 22.8 1.0
CA M:CYS597 4.6 23.2 1.0
FE2 M:SF4900 4.6 23.8 1.0
S1 M:SF4900 4.8 21.2 1.0
CA M:CYS595 4.9 23.6 1.0
CB M:CYS528 4.9 25.6 1.0
CD2 M:HIS516 5.0 23.5 1.0

Copper binding site 2 out of 4 in 3i04

Go back to Copper Binding Sites List in 3i04
Copper binding site 2 out of 4 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-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 Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu950

b:34.0
occ:1.00
SG N:CYS509 2.2 20.4 1.0
SG N:CYS595 2.3 25.2 1.0
SG N:CYS597 2.4 23.2 1.0
FE4 N:SF4900 2.9 23.3 1.0
S3 N:SF4900 2.9 20.9 1.0
C N:ACT953 2.9 71.2 1.0
NI N:NI951 3.0 24.4 1.0
CB N:CYS509 3.2 20.2 1.0
CB N:CYS595 3.6 25.2 1.0
O N:ACT953 3.7 71.2 1.0
CB N:CYS597 3.8 22.2 1.0
CH3 N:ACT953 3.9 71.2 1.0
CD1 N:ILE146 4.0 27.9 1.0
S2 N:SF4900 4.5 23.9 1.0
N N:CYS597 4.5 22.6 1.0
CA N:CYS509 4.5 22.1 1.0
FE1 N:SF4900 4.6 23.0 1.0
FE2 N:SF4900 4.7 23.6 1.0
CD1 N:LEU527 4.7 23.4 1.0
N N:GLY596 4.7 24.1 1.0
S1 N:SF4900 4.7 23.6 1.0
CA N:CYS597 4.8 21.9 1.0
CA N:CYS595 4.8 24.6 1.0

Copper binding site 3 out of 4 in 3i04

Go back to Copper Binding Sites List in 3i04
Copper binding site 3 out of 4 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-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 Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu950

b:73.3
occ:1.00
SG O:CYS509 2.0 54.4 1.0
SG O:CYS597 2.3 61.3 1.0
SG O:CYS595 2.7 63.1 1.0
C O:ACT953 3.0 0.1 1.0
FE4 O:SF4900 3.0 60.0 1.0
S3 O:SF4900 3.1 59.2 1.0
NI O:NI951 3.1 66.9 1.0
CB O:CYS509 3.2 55.3 1.0
O O:ACT953 3.3 0.1 1.0
CH3 O:ACT953 3.4 0.2 1.0
CB O:CYS597 3.8 59.5 1.0
CB O:CYS595 4.1 62.5 1.0
CD1 O:LEU527 4.4 56.8 1.0
CA O:CYS509 4.5 55.6 1.0
N O:CYS597 4.6 60.5 1.0
CD1 O:ILE146 4.6 46.3 1.0
CA O:CYS597 4.8 59.4 1.0
FE2 O:SF4900 4.8 61.6 1.0
S2 O:SF4900 4.8 57.8 1.0
FE1 O:SF4900 4.8 62.5 1.0
S1 O:SF4900 4.9 60.0 1.0
CB O:CYS528 4.9 60.3 1.0

Copper binding site 4 out of 4 in 3i04

Go back to Copper Binding Sites List in 3i04
Copper binding site 4 out of 4 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-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 Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cu950

b:49.3
occ:1.00
SG P:CYS509 2.1 36.7 1.0
SG P:CYS597 2.2 37.9 1.0
SG P:CYS595 2.5 41.8 1.0
C P:ACT953 2.9 76.1 1.0
FE4 P:SF4900 2.9 38.0 1.0
S3 P:SF4900 2.9 39.0 1.0
CB P:CYS509 3.1 36.1 1.0
NI P:NI951 3.1 41.2 1.0
CH3 P:ACT953 3.6 75.8 1.0
O P:ACT953 3.6 76.3 1.0
CB P:CYS597 3.6 37.7 1.0
CB P:CYS595 3.7 42.2 1.0
CD1 P:ILE146 4.4 36.4 1.0
CA P:CYS509 4.5 37.3 1.0
N P:CYS597 4.6 37.8 1.0
CD1 P:LEU527 4.6 37.8 1.0
S2 P:SF4900 4.6 41.8 1.0
FE1 P:SF4900 4.7 39.7 1.0
FE2 P:SF4900 4.7 41.4 1.0
CA P:CYS597 4.7 38.0 1.0
S1 P:SF4900 4.8 42.1 1.0
N P:GLY596 4.9 41.3 1.0
CA P:CYS595 5.0 41.9 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: Sun Dec 13 11:10:08 2020

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