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Nickel in PDB 7nys: Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A

Enzymatic activity of Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A

All present enzymatic activity of Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A:
2.3.1.169;

Protein crystallography data

The structure of Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A, PDB code: 7nys was solved by J.Kreibich, J.H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.56 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.276, 99.2, 238.584, 90, 90, 90
R / Rfree (%) 18.4 / 22.1

Other elements in 7nys:

The structure of Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A also contains other interesting chemical elements:

Titanium (Ti) 1 atom
Iron (Fe) 8 atoms
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A (pdb code 7nys). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A, PDB code: 7nys:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 7nys

Go back to Nickel Binding Sites List in 7nys
Nickel binding site 1 out of 4 in the Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni802

b:23.6
occ:1.00
NI A:UWE802 0.0 23.6 1.0
C A:UWE802 1.8 18.1 1.0
SG A:CYS600 2.3 24.0 1.0
SG A:CYS512 2.3 26.2 1.0
SG A:CYS598 2.4 24.2 1.0
NI A:NI803 2.8 20.9 1.0
HB3 A:CYS512 2.8 28.6 1.0
O A:UWE802 3.0 26.4 1.0
HB2 A:CYS598 3.1 24.5 1.0
CB A:CYS512 3.1 23.8 1.0
HB3 A:CYS600 3.2 23.8 1.0
CB A:CYS598 3.4 20.4 1.0
HD12 A:ILE149 3.4 44.2 1.0
CB A:CYS600 3.4 19.8 1.0
HB2 A:CYS512 3.6 28.6 1.0
HD13 A:ILE149 3.6 44.2 1.0
HG11 A:VAL152 3.6 30.0 1.0
HB3 A:CYS598 3.8 24.5 1.0
CD1 A:ILE149 3.9 36.8 1.0
FE4 A:SF4801 3.9 23.4 1.0
HB2 A:CYS600 4.1 23.8 1.0
HD11 A:ILE149 4.1 44.2 1.0
N A:CYS600 4.2 22.6 1.0
HD1 A:PHE232 4.2 27.8 1.0
N A:GLY599 4.3 18.4 1.0
S1 A:SF4801 4.4 25.4 1.0
HG21 A:VAL152 4.4 34.1 1.0
HA A:CYS512 4.4 34.8 1.0
HE1 A:PHE232 4.4 29.6 1.0
CA A:CYS512 4.5 29.0 1.0
CA A:CYS600 4.5 24.9 1.0
CG1 A:VAL152 4.5 25.0 1.0
HD11 A:LEU530 4.6 31.0 1.0
CA A:CYS598 4.6 19.4 1.0
CD1 A:PHE232 4.7 23.1 1.0
HA A:ILE149 4.7 26.5 1.0
CE1 A:PHE232 4.8 24.6 1.0
H A:CYS598 4.8 26.3 1.0
C A:CYS598 4.8 24.2 1.0
HG13 A:VAL152 4.8 30.0 1.0
HG12 A:VAL152 4.9 30.0 1.0

Nickel binding site 2 out of 4 in 7nys

Go back to Nickel Binding Sites List in 7nys
Nickel binding site 2 out of 4 in the Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni803

b:20.9
occ:1.00
N A:CYS600 2.0 22.6 1.0
N A:GLY599 2.1 18.4 1.0
SG A:CYS600 2.2 24.0 1.0
SG A:CYS598 2.2 24.2 1.0
NI A:UWE802 2.8 23.6 1.0
C A:GLY599 2.8 26.7 1.0
CA A:GLY599 2.9 19.2 1.0
CB A:CYS600 2.9 19.8 1.0
CA A:CYS600 2.9 24.9 1.0
CB A:CYS598 3.1 20.4 1.0
C A:CYS598 3.1 24.2 1.0
HB2 A:CYS598 3.1 24.5 1.0
HB3 A:CYS600 3.2 23.8 1.0
HD11 A:LEU530 3.2 31.0 1.0
H A:CYS598 3.3 26.3 1.0
H A:PHE601 3.4 23.1 1.0
HA3 A:GLY599 3.5 23.0 1.0
CA A:CYS598 3.5 19.4 1.0
C A:UWE802 3.5 18.1 1.0
HE1 A:PHE232 3.6 29.6 1.0
HA2 A:GLY599 3.6 23.0 1.0
C A:CYS600 3.7 22.0 1.0
HD1 A:PHE232 3.7 27.8 1.0
N A:CYS598 3.7 21.9 1.0
HA A:CYS600 3.8 29.8 1.0
N A:PHE601 3.8 19.3 1.0
HB2 A:CYS600 3.8 23.8 1.0
CD1 A:LEU530 3.9 25.8 1.0
HD13 A:LEU530 3.9 31.0 1.0
O A:GLY599 3.9 21.4 1.0
HB3 A:CYS598 4.0 24.5 1.0
HD12 A:LEU530 4.1 31.0 1.0
O A:CYS598 4.2 23.9 1.0
CE1 A:PHE232 4.3 24.6 1.0
CD1 A:PHE232 4.3 23.1 1.0
O A:UWE802 4.4 26.4 1.0
HA A:CYS598 4.4 23.2 1.0
O A:CYS600 4.6 20.7 1.0
HB3 A:SER597 4.8 24.4 1.0
HD2 A:PHE601 4.8 23.8 1.0
SG A:CYS512 4.9 26.2 1.0
S1 A:SF4801 4.9 25.4 1.0
HD13 A:ILE149 4.9 44.2 1.0
HD21 A:LEU530 4.9 30.7 1.0
HB3 A:CYS512 4.9 28.6 1.0
C A:SER597 4.9 23.9 1.0
CA A:PHE601 5.0 19.2 1.0
CD2 A:PHE601 5.0 19.8 1.0

Nickel binding site 3 out of 4 in 7nys

Go back to Nickel Binding Sites List in 7nys
Nickel binding site 3 out of 4 in the Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni802

b:20.2
occ:1.00
NI B:UWE802 0.0 20.2 1.0
C B:UWE802 1.8 12.4 1.0
SG B:CYS512 2.4 19.9 1.0
SG B:CYS600 2.4 20.4 1.0
SG B:CYS598 2.4 17.8 1.0
O B:UWE802 2.8 24.0 1.0
NI B:NI803 2.9 16.6 1.0
HB3 B:CYS512 3.0 19.0 1.0
HB3 B:CYS600 3.3 25.9 1.0
CB B:CYS512 3.3 15.8 1.0
HB2 B:CYS598 3.4 18.4 1.0
CB B:CYS600 3.5 21.6 1.0
HD12 B:ILE149 3.5 34.2 1.0
CB B:CYS598 3.6 15.3 1.0
HG11 B:VAL152 3.7 28.5 1.0
HB2 B:CYS512 3.7 19.0 1.0
FE4 B:SF4801 3.8 21.2 1.0
HB3 B:CYS598 4.0 18.4 1.0
HB2 B:CYS600 4.1 25.9 1.0
N B:CYS600 4.1 18.1 1.0
HD13 B:ILE149 4.1 34.2 1.0
CD1 B:ILE149 4.2 28.5 1.0
HD1 B:PHE232 4.2 27.2 1.0
S1 B:SF4801 4.3 19.6 1.0
HG13 B:VAL152 4.3 28.5 1.0
N B:GLY599 4.4 18.0 1.0
HG21 B:VAL152 4.4 27.7 1.0
CG1 B:VAL152 4.4 23.8 1.0
HA B:CYS512 4.4 20.8 1.0
CA B:CYS600 4.5 18.0 1.0
HA B:ILE149 4.5 22.7 1.0
CA B:CYS512 4.5 17.3 1.0
HE1 B:PHE232 4.6 22.6 1.0
HD11 B:ILE149 4.6 34.2 1.0
HD11 B:LEU530 4.6 26.2 1.0
CD1 B:PHE232 4.8 22.6 1.0
CA B:CYS598 4.8 14.6 1.0
H B:CYS598 4.9 17.9 1.0
C B:CYS598 5.0 16.1 1.0
CE1 B:PHE232 5.0 18.8 1.0

Nickel binding site 4 out of 4 in 7nys

Go back to Nickel Binding Sites List in 7nys
Nickel binding site 4 out of 4 in the Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Monomeric Acetyl-Coa Synthase in Closed Conformation with Carbon Monoxide Bound to the Ni Proximal of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni803

b:16.6
occ:1.00
N B:CYS600 1.8 18.1 1.0
N B:GLY599 2.1 18.0 1.0
SG B:CYS598 2.1 17.8 1.0
SG B:CYS600 2.2 20.4 1.0
C B:GLY599 2.7 18.9 1.0
CA B:GLY599 2.8 14.8 1.0
NI B:UWE802 2.9 20.2 1.0
CA B:CYS600 2.9 18.0 1.0
CB B:CYS600 3.0 21.6 1.0
HD11 B:LEU530 3.1 26.2 1.0
C B:CYS598 3.1 16.1 1.0
HB3 B:CYS600 3.2 25.9 1.0
CB B:CYS598 3.2 15.3 1.0
HB2 B:CYS598 3.4 18.4 1.0
HA3 B:GLY599 3.4 17.8 1.0
H B:PHE601 3.4 19.0 1.0
H B:CYS598 3.4 17.9 1.0
CA B:CYS598 3.5 14.6 1.0
HA2 B:GLY599 3.6 17.8 1.0
C B:UWE802 3.6 12.4 1.0
C B:CYS600 3.6 16.8 1.0
HA B:CYS600 3.7 21.6 1.0
HD1 B:PHE232 3.7 27.2 1.0
N B:PHE601 3.7 15.9 1.0
N B:CYS598 3.8 14.9 1.0
HE1 B:PHE232 3.8 22.6 1.0
CD1 B:LEU530 3.8 21.8 1.0
HB2 B:CYS600 3.9 25.9 1.0
O B:GLY599 3.9 17.0 1.0
HD12 B:LEU530 3.9 26.2 1.0
HD13 B:LEU530 4.0 26.2 1.0
HB3 B:CYS598 4.1 18.4 1.0
O B:CYS598 4.2 19.0 1.0
O B:UWE802 4.3 24.0 1.0
CD1 B:PHE232 4.4 22.6 1.0
HA B:CYS598 4.5 17.6 1.0
CE1 B:PHE232 4.5 18.8 1.0
O B:CYS600 4.7 20.4 1.0
HB3 B:SER597 4.7 20.7 1.0
HD2 B:PHE601 4.8 18.5 1.0
S1 B:SF4801 4.9 19.6 1.0
CA B:PHE601 4.9 16.5 1.0
C B:SER597 5.0 17.7 1.0
HA B:PHE601 5.0 19.8 1.0

Reference:

J.Kreibich, J.H.Jeoung, H.Dobbek. Ligand Binding at the Ni,Ni-[4FE-4S] Cluster of Acetyl-Coa Synthase To Be Published.
Page generated: Thu Oct 10 09:18:22 2024

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