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Copper in PDB 2z8y: Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica

Enzymatic activity of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica

All present enzymatic activity of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica:
1.2.7.4; 1.2.99.2; 2.3.1.169;

Protein crystallography data

The structure of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica, PDB code: 2z8y was solved by T.I.Doukov, L.C.Blasiak, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 2.51
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.540, 136.600, 141.750, 101.29, 109.22, 103.91
R / Rfree (%) 17.8 / 25

Other elements in 2z8y:

The structure of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica also contains other interesting chemical elements:

Nickel (Ni) 8 atoms
Xenon (Xe) 42 atoms
Iron (Fe) 56 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (pdb code 2z8y). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica, PDB code: 2z8y:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 2z8y

Go back to Copper Binding Sites List in 2z8y
Copper binding site 1 out of 4 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cu950

b:30.4
occ:1.00
 SG M:CYS597 2.1 20.9 1.0
SG M:CYS509 2.2 21.9 1.0
SG M:CYS595 2.3 20.2 1.0
S3 M:SF4900 2.8 20.6 1.0
NI M:NI951 3.0 18.4 1.0
FE4 M:SF4900 3.0 14.9 1.0
CB M:CYS509 3.2 19.3 1.0
CB M:CYS595 3.5 17.6 1.0
CB M:CYS597 3.6 18.6 1.0
XE M:XE1008 3.6 31.0 0.8
N M:CYS597 4.3 16.9 1.0
CD1 M:ILE146 4.3 13.2 1.0
CD1 M:LEU527 4.4 14.4 1.0
FE1 M:SF4900 4.5 13.4 1.0
CA M:CYS597 4.5 19.0 1.0
N M:GLY596 4.5 16.5 1.0
CA M:CYS509 4.6 20.2 1.0
S2 M:SF4900 4.6 15.2 1.0
FE2 M:SF4900 4.6 15.4 1.0
S1 M:SF4900 4.8 14.6 1.0
CA M:CYS595 4.8 17.5 1.0
CB M:CYS528 5.0 19.5 1.0

Copper binding site 2 out of 4 in 2z8y

Go back to Copper Binding Sites List in 2z8y
Copper binding site 2 out of 4 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu950

b:28.3
occ:1.00
 SG N:CYS509 2.2 17.6 1.0
SG N:CYS595 2.3 22.5 1.0
SG N:CYS597 2.4 18.9 1.0
NI N:NI951 2.9 18.0 1.0
S3 N:SF4900 3.0 17.4 1.0
FE4 N:SF4900 3.0 16.6 1.0
CB N:CYS509 3.2 16.8 1.0
CB N:CYS595 3.5 20.7 1.0
XE N:XE1009 3.7 34.8 0.7
CB N:CYS597 3.7 16.5 1.0
N N:CYS597 4.4 17.5 1.0
CD1 N:ILE146 4.6 25.8 1.0
FE1 N:SF4900 4.6 14.0 1.0
CA N:CYS509 4.6 18.0 1.0
N N:GLY596 4.6 17.8 1.0
FE2 N:SF4900 4.6 16.7 1.0
S2 N:SF4900 4.7 13.3 1.0
CD1 N:LEU527 4.7 14.6 1.0
CA N:CYS597 4.7 16.2 1.0
S1 N:SF4900 4.7 13.4 1.0
CA N:CYS595 4.8 20.6 1.0
CB N:CYS528 4.9 17.9 1.0
CD2 N:HIS516 5.0 9.4 1.0

Copper binding site 3 out of 4 in 2z8y

Go back to Copper Binding Sites List in 2z8y
Copper binding site 3 out of 4 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu950

b:88.5
occ:1.00
 XE O:XE1009 2.0 42.3 0.4
SG O:CYS597 2.5 55.8 1.0
SG O:CYS509 2.6 46.3 1.0
NI O:NI951 2.7 76.0 1.0
SG O:CYS595 2.7 62.8 1.0
CB O:CYS597 2.8 57.0 1.0
N O:CYS597 2.9 59.0 1.0
CB O:CYS509 3.4 50.3 1.0
CA O:CYS597 3.4 57.2 1.0
CB O:CYS595 3.4 57.9 1.0
N O:GLY596 3.8 60.8 1.0
C O:GLY596 3.9 59.6 1.0
C O:CYS595 4.1 59.9 1.0
CA O:GLY596 4.2 59.9 1.0
CA O:CYS595 4.3 59.1 1.0
CA O:CYS509 4.5 50.7 1.0
CD1 O:PHE229 4.6 50.0 1.0
C O:CYS597 4.7 56.3 1.0
CE1 O:PHE229 4.8 53.5 1.0
S3 O:SF4900 4.8 60.0 1.0
CG1 O:VAL149 4.9 54.9 1.0
O O:GLY596 4.9 59.8 1.0
O O:CYS595 4.9 60.6 1.0
FE4 O:SF4900 4.9 61.1 1.0

Copper binding site 4 out of 4 in 2z8y

Go back to Copper Binding Sites List in 2z8y
Copper binding site 4 out of 4 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cu950

b:52.6
occ:1.00
 SG P:CYS509 2.1 30.9 1.0
SG P:CYS595 2.3 41.3 1.0
SG P:CYS597 2.5 37.6 1.0
NI P:NI951 2.9 44.5 1.0
FE4 P:SF4900 3.0 31.9 1.0
S3 P:SF4900 3.0 33.5 1.0
CB P:CYS509 3.3 34.4 1.0
XE P:XE1009 3.5 31.9 0.5
CB P:CYS595 3.5 39.9 1.0
CB P:CYS597 3.9 32.9 1.0
CD1 P:LEU527 4.6 36.9 1.0
FE1 P:SF4900 4.6 37.5 1.0
S2 P:SF4900 4.7 35.4 1.0
CA P:CYS509 4.7 35.6 1.0
N P:CYS597 4.7 34.6 1.0
N P:GLY596 4.7 37.4 1.0
FE2 P:SF4900 4.7 32.6 1.0
CA P:CYS595 4.8 39.8 1.0
S1 P:SF4900 4.9 36.8 1.0
CA P:CYS597 4.9 33.6 1.0

Reference:

T.I.Doukov, L.C.Blasiak, J.Seravalli, S.W.Ragsdale, C.L.Drennan. Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase Biochemistry V. 47 3474 2008.
ISSN: ISSN 0006-2960
PubMed: 18293927
DOI: 10.1021/BI702386T
Page generated: Wed Jul 31 00:29:06 2024

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