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Nickel in PDB 1mjg: Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum)

Enzymatic activity of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum)

All present enzymatic activity of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum):
1.2.99.2;

Protein crystallography data

The structure of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum), PDB code: 1mjg was solved by T.I.Doukov, T.M.Iverson, J.Seravalli, S.W.Ragsdale, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.749, 136.973, 141.532, 101.45, 109.05, 103.94
R / Rfree (%) 21.5 / 24.1

Other elements in 1mjg:

The structure of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum) also contains other interesting chemical elements:

Iron (Fe) 56 atoms
Copper (Cu) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum) (pdb code 1mjg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum), PDB code: 1mjg:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 1mjg

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Nickel binding site 1 out of 8 in the Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni800

b:45.9
occ:1.00
 NI A:XCC800 0.0 45.9 1.0
SG A:CYS550 2.2 45.7 1.0
S1 A:XCC800 2.3 44.7 1.0
S4 A:XCC800 2.3 46.0 1.0
FE2 A:XCC800 2.7 39.4 1.0
FE3 A:XCC800 2.8 46.2 1.0
S3 A:XCC800 3.0 43.6 1.0
FE1 A:XCC800 3.1 42.7 1.0
FE4 A:XCC800 3.2 45.4 1.0
CB A:CYS550 3.8 34.9 1.0
S2 A:XCC800 4.2 44.3 1.0
SG A:CYS317 4.2 32.9 1.0
NE2 A:HIS283 4.3 35.4 1.0
NZ A:LYS587 4.3 21.7 1.0
OG A:SER585 4.6 27.5 1.0
O A:HOH803 4.7 24.2 1.0
SG A:CYS470 4.7 39.5 1.0
CE A:LYS587 4.8 23.2 1.0
CA A:CYS550 4.9 30.0 1.0
O A:GLY469 5.0 35.1 1.0

Nickel binding site 2 out of 8 in 1mjg

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Nickel binding site 2 out of 8 in the Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni800

b:42.6
occ:1.00
 NI B:XCC800 0.0 42.6 1.0
SG B:CYS550 2.2 43.0 1.0
S1 B:XCC800 2.3 43.0 1.0
S4 B:XCC800 2.3 43.1 1.0
FE2 B:XCC800 2.6 39.6 1.0
FE3 B:XCC800 2.8 44.1 1.0
S3 B:XCC800 3.0 41.0 1.0
FE1 B:XCC800 3.1 40.1 1.0
FE4 B:XCC800 3.2 43.5 1.0
CB B:CYS550 3.8 31.6 1.0
S2 B:XCC800 4.2 42.7 1.0
NZ B:LYS587 4.2 25.0 1.0
NE2 B:HIS283 4.3 35.4 1.0
SG B:CYS317 4.3 31.8 1.0
OG B:SER585 4.6 26.7 1.0
SG B:CYS470 4.7 37.9 1.0
CE B:LYS587 4.8 21.9 1.0
CA B:CYS550 4.9 24.7 1.0
O B:HOH831 4.9 27.3 1.0
O B:GLY469 5.0 36.1 1.0

Nickel binding site 3 out of 8 in 1mjg

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Nickel binding site 3 out of 8 in the Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni800

b:50.4
occ:1.00
 NI C:XCC800 0.0 50.4 1.0
SG C:CYS550 2.1 48.5 1.0
S1 C:XCC800 2.3 48.3 1.0
S4 C:XCC800 2.3 49.0 1.0
FE2 C:XCC800 2.6 42.6 1.0
FE3 C:XCC800 2.8 49.9 1.0
S3 C:XCC800 3.0 47.7 1.0
FE1 C:XCC800 3.2 47.6 1.0
FE4 C:XCC800 3.2 49.1 1.0
CB C:CYS550 3.8 38.3 1.0
NE2 C:HIS283 4.2 40.1 1.0
S2 C:XCC800 4.2 48.2 1.0
NZ C:LYS587 4.3 29.3 1.0
SG C:CYS317 4.3 36.6 1.0
OG C:SER585 4.6 36.2 1.0
CE C:LYS587 4.6 28.6 1.0
SG C:CYS470 4.7 45.6 1.0
CA C:CYS550 4.9 33.2 1.0

Nickel binding site 4 out of 8 in 1mjg

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Nickel binding site 4 out of 8 in the Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni800

b:54.2
occ:1.00
 NI D:XCC800 0.0 54.2 1.0
SG D:CYS550 2.2 52.9 1.0
S1 D:XCC800 2.3 53.0 1.0
S4 D:XCC800 2.3 53.2 1.0
FE2 D:XCC800 2.7 50.2 1.0
FE3 D:XCC800 2.8 54.0 1.0
S3 D:XCC800 2.9 52.6 1.0
FE1 D:XCC800 3.1 52.6 1.0
FE4 D:XCC800 3.1 53.5 1.0
CB D:CYS550 3.8 43.2 1.0
S2 D:XCC800 4.2 52.7 1.0
SG D:CYS317 4.3 44.7 1.0
NE2 D:HIS283 4.3 47.0 1.0
O D:HOH819 4.3 41.2 1.0
NZ D:LYS587 4.5 37.5 1.0
OG D:SER585 4.7 40.3 1.0
SG D:CYS470 4.7 48.9 1.0
CE D:LYS587 4.8 35.9 1.0
CA D:CYS550 4.9 38.2 1.0
O D:GLY469 4.9 45.6 1.0
O D:HOH908 4.9 35.5 1.0
CA D:GLY499 4.9 35.8 1.0

Nickel binding site 5 out of 8 in 1mjg

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Nickel binding site 5 out of 8 in the Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni902

b:9.8
occ:1.00
 N M:CYS597 1.8 19.0 1.0
N M:GLY596 1.9 21.2 1.0
SG M:CYS595 2.1 24.2 1.0
SG M:CYS597 2.2 25.2 1.0
C M:GLY596 2.6 19.2 1.0
CA M:GLY596 2.7 18.3 1.0
CU M:CU1901 2.8 17.9 1.0
CA M:CYS597 2.9 21.8 1.0
CB M:CYS597 2.9 19.9 1.0
C M:CYS595 3.0 21.8 1.0
CB M:CYS595 3.2 20.4 1.0
C M:ACT950 3.2 23.3 1.0
O M:ACT950 3.3 27.2 1.0
CA M:CYS595 3.5 22.8 1.0
N M:PHE598 3.7 24.4 1.0
C M:CYS597 3.7 23.2 1.0
N M:CYS595 3.8 24.4 1.0
CD1 M:LEU527 3.8 26.3 1.0
O M:GLY596 3.8 19.4 1.0
O M:CYS595 4.1 23.2 1.0
CH3 M:ACT950 4.2 24.6 1.0
CD2 M:PHE598 4.7 27.2 1.0
S3 M:SF4900 4.7 23.3 1.0
O M:CYS597 4.8 24.4 1.0
CD1 M:PHE229 4.9 33.4 1.0
CE1 M:PHE229 4.9 33.6 1.0
SG M:CYS509 4.9 24.9 1.0
CA M:PHE598 4.9 25.6 1.0

Nickel binding site 6 out of 8 in 1mjg

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Nickel binding site 6 out of 8 in the Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ni902

b:11.5
occ:1.00
 N N:CYS597 1.9 21.7 1.0
N N:GLY596 1.9 23.1 1.0
SG N:CYS595 2.2 24.8 1.0
SG N:CYS597 2.2 25.1 1.0
C N:GLY596 2.7 22.1 1.0
CA N:GLY596 2.7 21.8 1.0
CU N:CU1901 2.8 17.6 1.0
CA N:CYS597 2.9 20.7 1.0
CB N:CYS597 3.0 19.6 1.0
C N:CYS595 3.0 23.2 1.0
CB N:CYS595 3.1 20.2 1.0
C N:ACT950 3.1 24.1 1.0
CA N:CYS595 3.5 23.4 1.0
N N:PHE598 3.7 20.7 1.0
O N:ACT950 3.7 28.0 1.0
C N:CYS597 3.7 20.4 1.0
N N:CYS595 3.8 24.2 1.0
CD1 N:LEU527 3.8 26.4 1.0
O N:GLY596 3.8 22.3 1.0
CH3 N:ACT950 3.9 25.7 1.0
O N:CYS595 4.1 23.6 1.0
CD2 N:PHE598 4.7 21.7 1.0
S3 N:SF4900 4.7 24.5 1.0
O N:CYS597 4.8 20.4 1.0
CD1 N:PHE229 4.8 30.8 1.0
CE1 N:PHE229 4.9 31.4 1.0
CA N:PHE598 4.9 21.8 1.0
SG N:CYS509 5.0 23.0 1.0
C N:SER594 5.0 25.8 1.0

Nickel binding site 7 out of 8 in 1mjg

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Nickel binding site 7 out of 8 in the Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ni902

b:87.4
occ:1.00
 N O:CYS597 1.9 87.7 1.0
N O:GLY596 1.9 88.5 1.0
SG O:CYS595 2.2 88.0 1.0
SG O:CYS597 2.2 87.4 1.0
C O:GLY596 2.7 88.3 1.0
CA O:GLY596 2.7 88.5 1.0
CU O:CU1901 2.8 87.5 1.0
CA O:CYS597 2.9 87.2 1.0
CB O:CYS597 3.0 87.3 1.0
C O:CYS595 3.0 88.8 1.0
C O:ACT950 3.1 87.8 1.0
CB O:CYS595 3.2 88.4 1.0
CA O:CYS595 3.5 89.0 1.0
N O:PHE598 3.6 86.5 1.0
CD1 O:LEU527 3.6 91.0 1.0
O O:ACT950 3.6 88.3 1.0
C O:CYS597 3.6 86.8 1.0
N O:CYS595 3.7 89.5 1.0
O O:GLY596 3.9 88.3 1.0
CH3 O:ACT950 4.1 88.0 1.0
O O:CYS595 4.1 88.7 1.0
CD2 O:PHE598 4.5 85.9 1.0
S3 O:SF4900 4.6 88.7 1.0
O O:CYS597 4.7 86.6 1.0
CA O:PHE598 4.8 86.4 1.0
CD1 O:PHE229 4.9 70.7 1.0
C O:SER594 4.9 90.1 1.0
SG O:CYS509 5.0 87.3 1.0
CG O:LEU527 5.0 90.9 1.0
CE1 O:PHE229 5.0 71.7 1.0

Nickel binding site 8 out of 8 in 1mjg

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Nickel binding site 8 out of 8 in the Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (F. Clostridium Thermoaceticum) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ni902

b:49.1
occ:1.00
 N P:CYS597 1.9 50.4 1.0
N P:GLY596 1.9 52.4 1.0
SG P:CYS595 2.2 52.1 1.0
SG P:CYS597 2.2 51.1 1.0
C P:GLY596 2.7 51.5 1.0
CA P:GLY596 2.7 52.0 1.0
CU P:CU1901 2.8 49.6 1.0
CA P:CYS597 2.9 50.3 1.0
CB P:CYS597 3.0 50.1 1.0
C P:CYS595 3.0 52.8 1.0
C P:ACT950 3.1 50.7 1.0
CB P:CYS595 3.2 51.7 1.0
CA P:CYS595 3.5 53.0 1.0
N P:PHE598 3.7 49.6 1.0
O P:ACT950 3.7 51.7 1.0
C P:CYS597 3.7 50.1 1.0
N P:CYS595 3.8 53.6 1.0
CD1 P:LEU527 3.8 56.8 1.0
O P:GLY596 3.8 51.1 1.0
O P:CYS595 4.1 53.5 1.0
CH3 P:ACT950 4.1 50.4 1.0
S3 P:SF4900 4.7 49.6 1.0
CD2 P:PHE598 4.7 47.6 1.0
O P:CYS597 4.8 49.9 1.0
CD1 P:PHE229 4.8 40.8 1.0
SG P:CYS509 4.9 49.5 1.0
CE1 P:PHE229 4.9 42.0 1.0
CA P:PHE598 4.9 49.5 1.0
C P:SER594 5.0 55.0 1.0

Reference:

T.I.Doukov, T.M.Iverson, J.Seravalli, S.W.Ragsdale, C.L.Drennan. A Ni-Fe-Cu Center in A Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase Science V. 298 567 2002.
ISSN: ISSN 0036-8075
PubMed: 12386327
DOI: 10.1126/SCIENCE.1075843
Page generated: Wed Oct 9 15:02:08 2024

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