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Nickel 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:

Xenon (Xe) 42 atoms
Iron (Fe) 56 atoms
Copper (Cu) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 8 binding sites of Nickel 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 Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 2z8y

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Nickel binding site 1 out of 8 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 Nickel with other atoms in the Ni 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
A:Ni800

b:57.1
occ:1.00
 NI A:XCC800 0.0 57.1 1.0
SG A:CYS550 2.2 36.4 1.0
S4 A:XCC800 2.4 56.7 1.0
S1 A:XCC800 2.4 51.5 1.0
FE2 A:XCC800 2.9 37.6 1.0
FE3 A:XCC800 3.1 50.5 1.0
CB A:CYS550 3.3 22.9 1.0
FE1 A:XCC800 3.7 42.9 1.0
S3 A:XCC800 4.1 44.6 1.0
FE4 A:XCC800 4.2 48.5 1.0
NZ A:LYS587 4.3 17.4 1.0
OG A:SER585 4.3 9.9 1.0
O A:HOH1012 4.3 21.5 1.0
SG A:CYS317 4.4 23.7 1.0
S2 A:XCC800 4.4 49.0 1.0
NE2 A:HIS283 4.6 24.4 1.0
CA A:CYS550 4.6 21.0 1.0
CA A:GLY469 4.7 25.4 1.0
CB A:LYS587 4.9 12.9 1.0
CE A:LYS587 4.9 20.1 1.0
C A:GLY469 4.9 24.6 1.0
SG A:CYS470 4.9 27.1 1.0
CD A:LYS587 5.0 19.2 1.0

Nickel binding site 2 out of 8 in 2z8y

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Nickel binding site 2 out of 8 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 Nickel with other atoms in the Ni 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
B:Ni800

b:54.6
occ:1.00
 NI B:XCC800 0.0 54.6 1.0
SG B:CYS550 2.2 36.2 1.0
S4 B:XCC800 2.4 57.9 1.0
S1 B:XCC800 2.4 52.6 1.0
CB B:CYS550 3.0 19.3 1.0
FE2 B:XCC800 3.1 37.4 1.0
FE3 B:XCC800 3.2 52.7 1.0
NZ B:LYS587 3.7 17.4 1.0
FE1 B:XCC800 3.8 40.5 1.0
O B:HOH1023 4.1 20.2 1.0
S3 B:XCC800 4.3 45.5 1.0
FE4 B:XCC800 4.3 52.7 1.0
S2 B:XCC800 4.3 52.6 1.0
OG B:SER585 4.4 13.5 1.0
CA B:CYS550 4.4 19.6 1.0
CB B:LYS587 4.4 14.8 1.0
CE B:LYS587 4.5 18.1 1.0
NE2 B:HIS283 4.6 26.4 1.0
SG B:CYS317 4.6 19.6 1.0
CD B:LYS587 4.7 19.8 1.0
CD1 B:ILE591 4.7 12.8 1.0
CA B:GLY469 4.8 28.0 1.0

Nickel binding site 3 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 3 out of 8 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 Nickel with other atoms in the Ni 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
C:Ni800

b:66.2
occ:1.00
 NI C:XCC800 0.0 66.2 1.0
SG C:CYS550 1.8 42.9 1.0
S4 C:XCC800 2.3 64.4 1.0
S1 C:XCC800 2.4 66.1 1.0
FE2 C:XCC800 3.2 40.0 1.0
FE3 C:XCC800 3.3 61.2 1.0
CB C:CYS550 3.4 27.0 1.0
O C:HOH1021 3.7 24.3 1.0
FE1 C:XCC800 4.1 53.2 1.0
FE4 C:XCC800 4.2 54.3 1.0
CA C:GLY469 4.3 27.3 1.0
CA C:CYS550 4.4 25.8 1.0
OG C:SER585 4.4 21.8 1.0
NZ C:LYS587 4.4 22.9 1.0
SG C:CYS317 4.5 27.1 1.0
S3 C:XCC800 4.5 52.5 1.0
S2 C:XCC800 4.6 59.5 1.0
SG C:CYS470 4.7 31.3 1.0
CB C:LYS587 4.8 21.4 1.0
N C:GLY469 4.8 26.5 1.0
CD1 C:ILE591 4.9 8.8 1.0
C C:GLY469 4.9 27.1 1.0
N C:CYS550 4.9 23.7 1.0
CE C:LYS587 4.9 27.2 1.0
CA C:GLY499 5.0 21.0 1.0
NE2 C:HIS283 5.0 24.9 1.0

Nickel binding site 4 out of 8 in 2z8y

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Nickel binding site 4 out of 8 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 Nickel with other atoms in the Ni 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
D:Ni800

b:69.2
occ:1.00
 NI D:XCC800 0.0 69.2 1.0
SG D:CYS550 2.1 39.0 1.0
S4 D:XCC800 2.4 69.2 1.0
S1 D:XCC800 2.4 66.6 1.0
FE2 D:XCC800 3.1 52.5 1.0
FE3 D:XCC800 3.2 61.9 1.0
CB D:CYS550 3.5 25.8 1.0
FE1 D:XCC800 3.7 57.0 1.0
O D:HOH1013 4.0 20.7 1.0
FE4 D:XCC800 4.2 61.3 1.0
S3 D:XCC800 4.2 57.0 1.0
NZ D:LYS587 4.5 25.0 1.0
CB D:LYS587 4.5 22.3 1.0
S2 D:XCC800 4.5 61.8 1.0
CD D:LYS587 4.5 23.0 1.0
SG D:CYS317 4.5 33.4 1.0
OG D:SER585 4.5 21.6 1.0
NE2 D:HIS283 4.6 32.8 1.0
CA D:CYS550 4.7 24.2 1.0
SG D:CYS470 4.8 32.6 1.0
CA D:GLY469 4.8 30.7 1.0
CE D:LYS587 4.9 27.3 1.0

Nickel binding site 5 out of 8 in 2z8y

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Nickel binding site 5 out of 8 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 Nickel with other atoms in the Ni binding site number 5 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:Ni951

b:18.4
occ:1.00
 N M:CYS597 1.9 16.9 1.0
N M:GLY596 1.9 16.5 1.0
SG M:CYS597 2.1 20.9 1.0
SG M:CYS595 2.2 20.2 1.0
C M:GLY596 2.7 16.8 1.0
CA M:GLY596 2.7 16.5 1.0
CA M:CYS597 2.9 19.0 1.0
C M:CYS595 3.0 17.1 1.0
CU M:CU1950 3.0 30.4 1.0
CB M:CYS595 3.0 17.6 1.0
CB M:CYS597 3.1 18.6 1.0
CA M:CYS595 3.4 17.5 1.0
N M:PHE598 3.6 19.9 1.0
N M:CYS595 3.6 17.6 1.0
C M:CYS597 3.7 19.4 1.0
XE M:XE1008 3.8 31.0 0.8
O M:GLY596 3.9 18.3 1.0
CD1 M:LEU527 4.0 14.4 1.0
O M:CYS595 4.0 18.7 1.0
CD2 M:PHE598 4.4 23.9 1.0
CE2 M:PHE598 4.7 22.9 1.0
O M:CYS597 4.7 21.0 1.0
S3 M:SF4900 4.8 20.6 1.0
C M:SER594 4.9 18.6 1.0
CA M:PHE598 4.9 19.4 1.0
SG M:CYS509 4.9 21.9 1.0

Nickel binding site 6 out of 8 in 2z8y

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Nickel binding site 6 out of 8 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 Nickel with other atoms in the Ni binding site number 6 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:Ni951

b:18.0
occ:1.00
 N N:CYS597 1.9 17.5 1.0
N N:GLY596 2.1 17.8 1.0
SG N:CYS597 2.1 18.9 1.0
SG N:CYS595 2.2 22.5 1.0
C N:GLY596 2.8 17.3 1.0
CA N:GLY596 2.8 17.7 1.0
CU N:CU1950 2.9 28.3 1.0
CA N:CYS597 3.0 16.2 1.0
CB N:CYS597 3.0 16.5 1.0
CB N:CYS595 3.1 20.7 1.0
C N:CYS595 3.2 19.8 1.0
CA N:CYS595 3.5 20.6 1.0
N N:PHE598 3.7 14.8 1.0
C N:CYS597 3.7 16.1 1.0
N N:CYS595 3.8 20.2 1.0
XE N:XE1009 3.8 34.8 0.7
CD1 N:LEU527 3.9 14.6 1.0
O N:GLY596 4.0 16.7 1.0
O N:CYS595 4.3 23.1 1.0
CD2 N:PHE598 4.3 16.3 1.0
O N:CYS597 4.7 16.9 1.0
CE2 N:PHE598 4.7 14.1 1.0
S3 N:SF4900 4.8 17.4 1.0
CA N:PHE598 4.9 15.6 1.0
C N:SER594 4.9 20.7 1.0
SG N:CYS509 5.0 17.6 1.0

Nickel binding site 7 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 7 out of 8 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 Nickel with other atoms in the Ni binding site number 7 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:Ni951

b:76.0
occ:1.00
 N O:CYS597 1.9 59.0 1.0
N O:GLY596 2.4 60.8 1.0
SG O:CYS597 2.5 55.8 1.0
SG O:CYS595 2.6 62.8 1.0
CU O:CU1950 2.7 88.5 1.0
CA O:CYS597 2.7 57.2 1.0
C O:GLY596 2.9 59.6 1.0
CB O:CYS597 3.0 57.0 1.0
N O:PHE598 3.1 55.9 1.0
CA O:GLY596 3.2 59.9 1.0
C O:CYS597 3.2 56.3 1.0
C O:CYS595 3.3 59.9 1.0
CD1 O:LEU527 3.3 53.9 1.0
CB O:CYS595 3.4 57.9 1.0
CA O:CYS595 3.5 59.1 1.0
N O:CYS595 3.6 58.3 1.0
O O:GLY596 4.0 59.8 1.0
CA O:PHE598 4.2 56.3 1.0
O O:CYS597 4.2 56.0 1.0
SG O:CYS509 4.3 46.3 1.0
CD2 O:PHE598 4.4 57.3 1.0
O O:CYS595 4.5 60.6 1.0
XE O:XE1009 4.5 42.3 0.4
CB O:PHE598 4.6 56.5 1.0
CG O:PHE598 4.6 57.5 1.0
S3 O:SF4900 4.6 60.0 1.0
CG O:LEU527 4.7 55.3 1.0
C O:SER594 4.7 58.3 1.0

Nickel binding site 8 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 8 out of 8 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 Nickel with other atoms in the Ni binding site number 8 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:Ni951

b:44.5
occ:1.00
 SG P:CYS595 2.0 41.3 1.0
N P:CYS597 2.0 34.6 1.0
SG P:CYS597 2.1 37.6 1.0
N P:GLY596 2.2 37.4 1.0
CB P:CYS597 2.8 32.9 1.0
C P:GLY596 2.9 34.2 1.0
CU P:CU1950 2.9 52.6 1.0
CA P:CYS597 2.9 33.6 1.0
CA P:GLY596 3.0 35.2 1.0
CB P:CYS595 3.1 39.9 1.0
C P:CYS595 3.2 38.4 1.0
XE P:XE1009 3.5 31.9 0.5
CA P:CYS595 3.6 39.8 1.0
C P:CYS597 3.8 32.8 1.0
N P:PHE598 3.9 31.4 1.0
N P:CYS595 4.0 39.8 1.0
CD1 P:LEU527 4.1 36.9 1.0
O P:GLY596 4.1 33.9 1.0
O P:CYS595 4.3 39.2 1.0
CD2 P:PHE598 4.7 23.4 1.0
O P:CYS597 4.8 33.8 1.0
S3 P:SF4900 4.8 33.5 1.0
SG P:CYS509 4.8 30.9 1.0
CE2 P:PHE598 4.9 27.7 1.0
CE1 P:PHE229 5.0 30.9 1.0
CD1 P:PHE229 5.0 30.7 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 Oct 9 17:08:45 2024

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