Atomistry » Copper » PDB 3f00-3ie9 » 3i04
Atomistry »
  Copper »
    PDB 3f00-3ie9 »
      3i04 »

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: Wed Jul 31 01:05:07 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy