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Nickel in PDB 1oao: Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase

Enzymatic activity of Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase

All present enzymatic activity of Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase:
1.2.7.4; 1.2.99.2; 2.3.1.169;

Protein crystallography data

The structure of Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase, PDB code: 1oao was solved by C.Darnault, A.Volbeda, E.J.Kim, P.Legrand, X.Vernede, P.A.Lindahl, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 244.570, 81.890, 167.220, 90.00, 96.19, 90.00
R / Rfree (%) 14.7 / 17.9

Other elements in 1oao:

The structure of Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase also contains other interesting chemical elements:

Iron (Fe) 30 atoms
Zinc (Zn) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase (pdb code 1oao). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase, PDB code: 1oao:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 1oao

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Nickel binding site 1 out of 6 in the Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1677

b:23.3
occ:0.50
NI A:XCC1677 0.0 23.3 0.5
C A:FOR1678 1.7 23.3 0.5
S1 A:XCC1677 2.3 17.7 0.8
S2 A:XCC1677 2.3 19.5 0.8
SG A:CYS550 2.3 14.5 0.5
FE4 A:XCC1677 2.7 19.9 0.8
O A:FOR1678 2.8 23.5 0.5
SG A:CYS550 3.3 13.8 0.2
CB A:CYS550 3.5 10.9 0.2
CB A:CYS550 3.5 11.0 0.5
FE1 A:XCC1677 3.6 24.4 0.7
FE A:FE21700 3.6 22.5 0.3
CB A:CYS550 3.6 11.0 0.2
FE2 A:XCC1677 3.7 17.9 0.8
FE3 A:XCC1677 3.9 18.3 0.8
O A:HOH2258 4.1 15.7 1.0
SG A:CYS550 4.3 13.0 0.2
CA A:GLY469 4.3 17.6 1.0
SG A:CYS470 4.3 21.4 1.0
S4 A:XCC1677 4.4 17.7 0.8
OG A:SER585 4.6 17.6 1.0
C A:GLY469 4.6 17.9 1.0
S3 A:XCC1677 4.7 17.5 0.8
NZ A:LYS587 4.7 21.2 1.0
N A:GLY469 4.8 16.0 1.0
CA A:CYS550 4.8 11.1 1.0
CB A:LYS587 4.8 11.6 1.0
CE A:LYS587 4.9 20.9 1.0
SG A:CYS317 4.9 17.6 1.0
NE2 A:HIS283 4.9 20.3 1.0
N A:CYS470 5.0 18.8 1.0

Nickel binding site 2 out of 6 in 1oao

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Nickel binding site 2 out of 6 in the Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1677

b:23.6
occ:0.50
NI B:XCC1677 0.0 23.6 0.5
C B:FOR1678 1.7 23.8 0.5
S1 B:XCC1677 2.3 19.9 0.8
SG B:CYS550 2.3 16.2 0.5
S4 B:XCC1677 2.4 18.8 0.8
FE3 B:XCC1677 2.7 17.1 0.8
O B:FOR1678 2.8 24.1 0.5
SG B:CYS550 3.4 16.5 0.2
FE2 B:XCC1677 3.5 22.0 0.7
CB B:CYS550 3.5 12.9 0.2
CB B:CYS550 3.5 13.0 0.5
CB B:CYS550 3.6 13.0 0.2
FE B:FE21700 3.6 20.5 0.3
FE1 B:XCC1677 3.8 17.6 0.8
FE4 B:XCC1677 4.0 18.4 0.8
O B:HOH2271 4.0 12.3 1.0
SG B:CYS550 4.3 14.8 0.2
SG B:CYS470 4.3 19.6 1.0
S3 B:XCC1677 4.4 17.1 0.8
CA B:GLY469 4.4 16.8 1.0
OG B:SER585 4.6 15.2 1.0
NZ B:LYS587 4.6 20.4 1.0
C B:GLY469 4.7 17.2 1.0
S2 B:XCC1677 4.7 17.4 0.8
N B:GLY469 4.7 15.5 1.0
CA B:CYS550 4.8 13.3 1.0
CB B:LYS587 4.8 11.0 1.0
CD1 B:ILE591 4.9 6.8 1.0
CE B:LYS587 4.9 14.9 1.0
NE2 B:HIS283 4.9 19.0 1.0
N B:CYS470 5.0 18.0 1.0
SG B:CYS317 5.0 17.5 1.0

Nickel binding site 3 out of 6 in 1oao

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Nickel binding site 3 out of 6 in the Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni1732

b:9.2
occ:1.00
N C:CYS597 2.0 8.3 1.0
N C:GLY596 2.0 8.5 1.0
SG C:CYS597 2.2 7.0 1.0
SG C:CYS595 2.2 9.3 1.0
C C:GLY596 2.8 9.2 1.0
CA C:GLY596 2.8 9.0 1.0
ZN C:ZN1731 2.8 12.4 1.0
CA C:CYS597 2.9 7.5 1.0
CB C:CYS597 3.0 7.0 1.0
C C:CYS595 3.0 9.1 1.0
CB C:CYS595 3.1 7.1 1.0
CA C:CYS595 3.4 8.7 1.0
C C:CYS597 3.7 7.2 1.0
N C:CYS595 3.7 7.0 1.0
N C:PHE598 3.7 6.1 1.0
S C:SX1733 3.8 18.0 1.0
CD1 C:LEU527 3.8 8.1 1.0
O C:SX1733 3.9 15.1 1.0
O C:GLY596 4.0 8.7 1.0
O C:CYS595 4.2 9.7 1.0
CD2 C:PHE229 4.4 9.0 1.0
O C:CYS597 4.7 8.2 1.0
CD2 C:PHE598 4.7 8.8 1.0
CE2 C:PHE229 4.7 7.6 1.0
S1 C:SF41730 4.9 7.3 1.0
C C:SER594 5.0 8.2 1.0
CA C:PHE598 5.0 7.3 1.0

Nickel binding site 4 out of 6 in 1oao

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Nickel binding site 4 out of 6 in the Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1731

b:17.3
occ:0.70
NI D:NI1731 0.0 17.3 0.7
NI D:NI1731 1.7 16.9 0.3
SG D:CYS597 2.1 12.5 1.0
SG D:CYS509 2.3 10.6 1.0
SG D:CYS595 2.3 9.4 1.0
OXT D:ACT1733 2.4 18.4 0.7
FE4 D:SF41730 2.7 9.8 1.0
S1 D:SF41730 3.0 9.0 1.0
NI D:NI1732 3.0 10.0 1.0
C D:ACT1733 3.4 19.2 0.7
CB D:CYS509 3.4 7.4 1.0
CB D:CYS597 3.5 10.3 1.0
CB D:CYS595 3.7 9.1 1.0
CZ D:PHE512 3.8 11.2 1.0
CH3 D:ACT1733 4.0 18.8 0.7
O D:ACT1733 4.3 20.0 0.7
S3 D:SF41730 4.3 11.1 1.0
FE2 D:SF41730 4.4 10.2 1.0
CE1 D:PHE512 4.4 10.7 1.0
N D:CYS597 4.4 9.9 1.0
CD2 D:LEU527 4.5 10.7 1.0
CB D:CYS528 4.5 10.9 1.0
S2 D:SF41730 4.6 9.6 1.0
CA D:CYS597 4.6 10.5 1.0
FE3 D:SF41730 4.6 10.4 1.0
CE2 D:PHE512 4.7 10.4 1.0
N D:GLY596 4.8 9.9 1.0
CA D:CYS509 4.8 7.9 1.0
CA D:CYS595 5.0 9.1 1.0

Nickel binding site 5 out of 6 in 1oao

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Nickel binding site 5 out of 6 in the Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1731

b:16.9
occ:0.30
NI D:NI1731 0.0 16.9 0.3
NI D:NI1731 1.7 17.3 0.7
CZ D:PHE512 2.1 11.2 1.0
SG D:CYS509 2.4 10.6 1.0
SG D:CYS595 2.5 9.4 1.0
CE1 D:PHE512 2.9 10.7 1.0
NI D:NI1732 2.9 10.0 1.0
CB D:CYS509 2.9 7.4 1.0
CB D:CYS595 3.0 9.1 1.0
SG D:CYS597 3.1 12.5 1.0
CE2 D:PHE512 3.1 10.4 1.0
OXT D:ACT1733 3.3 18.4 0.7
FE4 D:SF41730 3.8 9.8 1.0
CB D:CYS597 3.8 10.3 1.0
CH3 D:ACT1733 3.9 18.8 0.7
C D:ACT1733 3.9 19.2 0.7
N D:GLY596 4.1 9.9 1.0
CD1 D:PHE512 4.2 10.5 1.0
CA D:CYS509 4.2 7.9 1.0
N D:CYS597 4.3 9.9 1.0
CA D:CYS595 4.3 9.1 1.0
CD2 D:PHE512 4.3 11.7 1.0
S1 D:SF41730 4.6 9.0 1.0
C D:CYS595 4.6 9.3 1.0
CA D:CYS597 4.7 10.5 1.0
CG D:PHE512 4.8 9.0 1.0
O D:CYS509 4.8 7.0 1.0
CA D:GLY596 5.0 9.8 1.0

Nickel binding site 6 out of 6 in 1oao

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Nickel binding site 6 out of 6 in the Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Nizn[FE4S4] and Nini[FE4S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1732

b:10.0
occ:1.00
N D:CYS597 2.0 9.9 1.0
N D:GLY596 2.0 9.9 1.0
SG D:CYS595 2.2 9.4 1.0
SG D:CYS597 2.3 12.5 1.0
C D:GLY596 2.8 10.2 1.0
CA D:GLY596 2.9 9.8 1.0
NI D:NI1731 2.9 16.9 0.3
CB D:CYS595 2.9 9.1 1.0
CA D:CYS597 3.0 10.5 1.0
C D:CYS595 3.0 9.3 1.0
CB D:CYS597 3.0 10.3 1.0
NI D:NI1731 3.0 17.3 0.7
CA D:CYS595 3.3 9.1 1.0
N D:CYS595 3.6 9.4 1.0
N D:PHE598 3.7 9.4 1.0
C D:CYS597 3.7 10.0 1.0
CD2 D:LEU527 3.8 10.7 1.0
O D:GLY596 4.0 10.2 1.0
CZ D:PHE512 4.0 11.2 1.0
O D:CYS595 4.1 8.8 1.0
CE2 D:PHE512 4.2 10.4 1.0
CD2 D:PHE598 4.4 10.3 1.0
CE2 D:PHE598 4.7 10.0 1.0
OXT D:ACT1733 4.7 18.4 0.7
O D:CYS597 4.7 10.6 1.0
S1 D:SF41730 4.8 9.0 1.0
C D:SER594 4.9 9.2 1.0
CA D:PHE598 4.9 9.7 1.0

Reference:

C.Darnault, A.Volbeda, E.J.Kim, P.Legrand, X.Vernede, P.A.Lindahl, J.C.Fontecilla-Camps. Ni-Zn-[FE4-S4] and Ni-Ni-[FE4-S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase Nat.Struct.Biol. V. 10 271 2003.
ISSN: ISSN 1072-8368
PubMed: 12627225
DOI: 10.1038/NSB912
Page generated: Wed Dec 16 01:13:52 2020

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