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Iron in PDB 7nz5: Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A

Enzymatic activity of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A

All present enzymatic activity of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A:
2.3.1.169;

Protein crystallography data

The structure of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A, PDB code: 7nz5 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) 46.19 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.246, 98.811, 238.875, 90, 90, 90
R / Rfree (%) 19.3 / 22.4

Other elements in 7nz5:

The structure of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Titanium (Ti) 1 atom
Nickel (Ni) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A (pdb code 7nz5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A, PDB code: 7nz5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7nz5

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Iron binding site 1 out of 8 in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:14.8
occ:1.00
FE1 A:SF4801 0.0 14.8 1.0
S2 A:SF4801 2.3 15.0 1.0
S4 A:SF4801 2.3 14.9 1.0
S3 A:SF4801 2.3 14.5 1.0
SG A:CYS509 2.4 20.2 1.0
HB3 A:CYS509 2.7 15.8 1.0
FE4 A:SF4801 2.7 16.0 1.0
FE2 A:SF4801 2.7 15.7 1.0
FE3 A:SF4801 2.7 15.2 1.0
CB A:CYS509 3.0 13.1 1.0
HB3 A:LEU511 3.3 17.4 1.0
HB2 A:CYS509 3.5 15.8 1.0
H A:LEU511 3.6 23.6 1.0
HG13 A:ILE534 3.6 26.7 1.0
S1 A:SF4801 3.8 16.9 1.0
HB2 A:CYS521 3.9 21.9 1.0
HB2 A:LEU511 4.1 17.4 1.0
CB A:LEU511 4.1 14.4 1.0
H A:CYS512 4.2 15.8 1.0
CA A:CYS509 4.3 15.0 1.0
N A:LEU511 4.3 19.6 1.0
C A:CYS509 4.3 15.9 1.0
O A:CYS509 4.4 17.5 1.0
HD23 A:LEU511 4.4 20.9 1.0
CG1 A:ILE534 4.5 22.2 1.0
HB A:ILE534 4.6 20.4 1.0
CB A:CYS521 4.6 18.1 1.0
HB3 A:CYS521 4.6 21.9 1.0
HG21 A:ILE534 4.7 17.8 1.0
HA A:CYS509 4.7 18.2 1.0
HD21 A:ASN551 4.7 20.6 1.0
HG12 A:ILE534 4.8 26.7 1.0
CA A:LEU511 4.8 12.2 1.0
HB2 A:CYS512 4.8 21.4 1.0
N A:CYS512 4.8 13.1 1.0
SG A:CYS512 4.9 18.2 1.0
SG A:CYS521 4.9 15.6 1.0
N A:LEU510 4.9 18.1 1.0
HD11 A:ILE149 4.9 32.7 1.0

Iron binding site 2 out of 8 in 7nz5

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Iron binding site 2 out of 8 in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:15.7
occ:1.00
FE2 A:SF4801 0.0 15.7 1.0
S1 A:SF4801 2.3 16.9 1.0
S4 A:SF4801 2.3 14.9 1.0
S3 A:SF4801 2.3 14.5 1.0
SG A:CYS521 2.5 15.6 1.0
FE1 A:SF4801 2.7 14.8 1.0
FE4 A:SF4801 2.7 16.0 1.0
FE3 A:SF4801 2.8 15.2 1.0
HB2 A:CYS521 2.8 21.9 1.0
CB A:CYS521 3.1 18.1 1.0
HE2 A:HIS519 3.2 21.1 1.0
HB3 A:CYS521 3.4 21.9 1.0
HB3 A:CYS509 3.5 15.8 1.0
HG A:LEU530 3.5 20.0 1.0
S2 A:SF4801 3.9 15.0 1.0
H A:LEU530 3.9 14.1 1.0
NE2 A:HIS519 4.1 17.5 1.0
HA3 A:GLY529 4.2 18.4 1.0
H A:CYS531 4.2 12.5 1.0
CB A:CYS509 4.4 13.1 1.0
CG A:LEU530 4.4 16.6 1.0
HD23 A:LEU530 4.4 22.7 1.0
HD11 A:LEU530 4.5 22.1 1.0
CA A:CYS521 4.5 14.7 1.0
HD21 A:LEU530 4.6 22.7 1.0
HA2 A:GLY529 4.6 18.4 1.0
N A:LEU530 4.6 11.6 1.0
HD2 A:HIS519 4.6 16.3 1.0
HB2 A:CYS512 4.7 21.4 1.0
SG A:CYS509 4.7 20.2 1.0
HB3 A:CYS531 4.7 20.6 1.0
H A:CYS521 4.7 17.2 1.0
CD2 A:LEU530 4.7 18.8 1.0
HB2 A:CYS509 4.8 15.8 1.0
O A:CYS509 4.8 17.5 1.0
CA A:GLY529 4.8 15.2 1.0
CD2 A:HIS519 4.8 13.5 1.0
HA A:CYS521 4.8 17.8 1.0
O A:HOH1431 4.9 21.2 1.0
CD1 A:LEU530 4.9 18.4 1.0
SG A:CYS531 4.9 17.0 1.0
HD12 A:LEU530 5.0 22.1 1.0
N A:CYS521 5.0 14.2 1.0

Iron binding site 3 out of 8 in 7nz5

Go back to Iron Binding Sites List in 7nz5
Iron binding site 3 out of 8 in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:15.2
occ:1.00
FE3 A:SF4801 0.0 15.2 1.0
S4 A:SF4801 2.3 14.9 1.0
S2 A:SF4801 2.3 15.0 1.0
S1 A:SF4801 2.3 16.9 1.0
SG A:CYS531 2.5 17.0 1.0
FE1 A:SF4801 2.7 14.8 1.0
FE4 A:SF4801 2.7 16.0 1.0
FE2 A:SF4801 2.8 15.7 1.0
HB3 A:CYS531 2.8 20.6 1.0
CB A:CYS531 3.2 17.1 1.0
H A:CYS531 3.3 12.5 1.0
HG13 A:ILE534 3.7 26.7 1.0
HD11 A:ILE149 3.8 32.7 1.0
O A:HOH1654 3.8 29.1 1.0
HG12 A:ILE534 3.8 26.7 1.0
HB2 A:CYS531 3.9 20.6 1.0
S3 A:SF4801 3.9 14.5 1.0
HB A:ILE534 4.0 20.4 1.0
HD13 A:ILE149 4.0 32.7 1.0
HA3 A:GLY529 4.1 18.4 1.0
N A:CYS531 4.1 10.3 1.0
CG1 A:ILE534 4.1 22.2 1.0
CA A:CYS531 4.3 10.7 1.0
CD1 A:ILE149 4.4 27.2 1.0
HG A:LEU530 4.5 20.0 1.0
H A:LEU530 4.6 14.1 1.0
CB A:ILE534 4.6 16.9 1.0
H A:GLY532 4.8 18.5 1.0
H A:ALA533 4.8 26.4 1.0
HB3 A:CYS509 4.8 15.8 1.0
C A:GLY529 4.8 11.7 1.0
H A:ILE534 4.9 20.9 1.0
N A:LEU530 4.9 11.6 1.0
CA A:GLY529 4.9 15.2 1.0
HD12 A:ILE149 4.9 32.7 1.0
SG A:CYS509 4.9 20.2 1.0
HA A:CYS531 5.0 13.0 1.0
SG A:CYS512 5.0 18.2 1.0

Iron binding site 4 out of 8 in 7nz5

Go back to Iron Binding Sites List in 7nz5
Iron binding site 4 out of 8 in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:16.0
occ:1.00
FE4 A:SF4801 0.0 16.0 1.0
S2 A:SF4801 2.3 15.0 1.0
S1 A:SF4801 2.3 16.9 1.0
S3 A:SF4801 2.3 14.5 1.0
SG A:CYS512 2.5 18.2 1.0
FE1 A:SF4801 2.7 14.8 1.0
FE2 A:SF4801 2.7 15.7 1.0
FE3 A:SF4801 2.7 15.2 1.0
HB2 A:CYS512 3.0 21.4 1.0
CB A:CYS512 3.3 17.7 1.0
H A:CYS512 3.5 15.8 1.0
ZN A:ZN802 3.8 9.2 0.6
HD11 A:ILE149 3.8 32.7 1.0
HB3 A:LEU511 3.8 17.4 1.0
S4 A:SF4801 3.9 14.9 1.0
HD13 A:ILE149 3.9 32.7 1.0
N A:CYS512 4.0 13.1 1.0
HB3 A:CYS512 4.1 21.4 1.0
HB3 A:CYS531 4.1 20.6 1.0
HD12 A:ILE149 4.1 32.7 1.0
CD1 A:ILE149 4.1 27.2 1.0
SG A:CYS600 4.3 16.9 1.0
CA A:CYS512 4.3 19.0 1.0
SG A:CYS598 4.3 19.7 1.0
HE2 A:HIS519 4.6 21.1 1.0
HA A:CYS512 4.6 22.9 1.0
HD23 A:LEU511 4.6 20.9 1.0
HD2 A:HIS519 4.7 16.3 1.0
HG21 A:VAL152 4.7 22.9 1.0
O A:HOH1411 4.8 16.0 1.0
CB A:LEU511 4.8 14.4 1.0
H A:LEU511 4.8 23.6 1.0
SG A:CYS509 4.9 20.2 1.0
HD11 A:LEU530 4.9 22.1 1.0
HB3 A:CYS509 4.9 15.8 1.0
HB2 A:CYS521 4.9 21.9 1.0
C A:LEU511 4.9 12.3 1.0
CB A:CYS531 4.9 17.1 1.0
SG A:CYS531 5.0 17.0 1.0

Iron binding site 5 out of 8 in 7nz5

Go back to Iron Binding Sites List in 7nz5
Iron binding site 5 out of 8 in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:13.2
occ:1.00
FE1 B:SF4801 0.0 13.2 1.0
S3 B:SF4801 2.3 12.4 1.0
S4 B:SF4801 2.3 13.4 1.0
S2 B:SF4801 2.3 12.7 1.0
SG B:CYS509 2.4 18.1 1.0
FE2 B:SF4801 2.7 14.6 1.0
FE4 B:SF4801 2.7 12.8 1.0
FE3 B:SF4801 2.7 12.7 1.0
HB3 B:CYS509 2.8 12.8 1.0
CB B:CYS509 3.1 10.6 1.0
HB3 B:LEU511 3.3 18.0 1.0
HG13 B:ILE534 3.6 26.8 1.0
HB2 B:CYS509 3.6 12.8 1.0
H B:LEU511 3.7 12.7 1.0
S1 B:SF4801 3.9 16.5 1.0
HB2 B:CYS521 3.9 17.3 1.0
HB2 B:LEU511 4.1 18.0 1.0
CB B:LEU511 4.2 14.9 1.0
H B:CYS512 4.3 14.0 1.0
CA B:CYS509 4.3 7.5 1.0
HD23 B:LEU511 4.4 26.7 1.0
C B:CYS509 4.4 13.3 1.0
N B:LEU511 4.4 10.5 1.0
CG1 B:ILE534 4.5 22.2 1.0
O B:CYS509 4.5 15.8 1.0
HB B:ILE534 4.6 17.1 1.0
HD21 B:ASN551 4.7 15.9 1.0
CB B:CYS521 4.7 14.3 1.0
HG21 B:ILE534 4.7 15.6 1.0
HG12 B:ILE534 4.7 26.8 1.0
HA B:CYS509 4.8 9.1 1.0
HB3 B:CYS521 4.8 17.3 1.0
SG B:CYS512 4.8 16.0 1.0
SG B:CYS521 4.8 18.2 1.0
CA B:LEU511 4.9 11.3 1.0
N B:CYS512 4.9 11.5 1.0
HD22 B:LEU511 4.9 26.7 1.0
HB2 B:CYS512 4.9 13.8 1.0
N B:LEU510 5.0 15.0 1.0

Iron binding site 6 out of 8 in 7nz5

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Iron binding site 6 out of 8 in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:14.6
occ:1.00
FE2 B:SF4801 0.0 14.6 1.0
S3 B:SF4801 2.3 12.4 1.0
S4 B:SF4801 2.3 13.4 1.0
S1 B:SF4801 2.3 16.5 1.0
SG B:CYS521 2.5 18.2 1.0
FE1 B:SF4801 2.7 13.2 1.0
FE4 B:SF4801 2.7 12.8 1.0
FE3 B:SF4801 2.7 12.7 1.0
HB2 B:CYS521 2.9 17.3 1.0
HE2 B:HIS519 3.2 21.7 1.0
CB B:CYS521 3.2 14.3 1.0
HB3 B:CYS521 3.5 17.3 1.0
HB3 B:CYS509 3.6 12.8 1.0
HG B:LEU530 3.6 12.8 1.0
S2 B:SF4801 3.9 12.7 1.0
NE2 B:HIS519 4.0 18.0 1.0
H B:LEU530 4.1 18.1 1.0
H B:CYS531 4.1 14.7 1.0
HA3 B:GLY529 4.2 24.9 1.0
HD21 B:LEU530 4.4 16.6 1.0
CB B:CYS509 4.5 10.6 1.0
CG B:LEU530 4.5 10.5 1.0
HA2 B:GLY529 4.6 24.9 1.0
CA B:CYS521 4.6 10.7 1.0
HD2 B:HIS519 4.6 12.9 1.0
HB3 B:CYS531 4.6 18.2 1.0
H B:CYS521 4.7 13.7 1.0
N B:LEU530 4.7 14.9 1.0
SG B:CYS509 4.8 18.1 1.0
O B:HOH1325 4.8 16.6 1.0
CD2 B:HIS519 4.8 10.7 1.0
HD23 B:LEU530 4.8 16.6 1.0
CA B:GLY529 4.8 20.6 1.0
HB2 B:CYS512 4.8 13.8 1.0
HD11 B:LEU530 4.8 17.0 1.0
CD2 B:LEU530 4.8 13.8 1.0
O B:CYS509 4.9 15.8 1.0
HB2 B:CYS509 4.9 12.8 1.0
N B:CYS521 4.9 11.3 1.0
HA B:CYS521 4.9 12.9 1.0
SG B:CYS531 4.9 18.1 1.0

Iron binding site 7 out of 8 in 7nz5

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Iron binding site 7 out of 8 in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:12.7
occ:1.00
FE3 B:SF4801 0.0 12.7 1.0
S4 B:SF4801 2.3 13.4 1.0
S2 B:SF4801 2.3 12.7 1.0
S1 B:SF4801 2.3 16.5 1.0
SG B:CYS531 2.5 18.1 1.0
FE4 B:SF4801 2.7 12.8 1.0
FE1 B:SF4801 2.7 13.2 1.0
FE2 B:SF4801 2.7 14.6 1.0
HB3 B:CYS531 2.8 18.2 1.0
CB B:CYS531 3.2 15.1 1.0
H B:CYS531 3.3 14.7 1.0
HD11 B:ILE149 3.4 27.0 1.0
HG13 B:ILE534 3.6 26.8 1.0
HG12 B:ILE534 3.7 26.8 1.0
HB2 B:CYS531 3.9 18.2 1.0
HA3 B:GLY529 3.9 24.9 1.0
S3 B:SF4801 3.9 12.4 1.0
HB B:ILE534 4.0 17.1 1.0
N B:CYS531 4.0 12.1 1.0
CG1 B:ILE534 4.1 22.2 1.0
CA B:CYS531 4.3 13.8 1.0
CD1 B:ILE149 4.3 22.4 1.0
HD13 B:ILE149 4.5 27.0 1.0
HG B:LEU530 4.6 12.8 1.0
CB B:ILE534 4.6 14.2 1.0
HD12 B:ILE149 4.6 27.0 1.0
H B:ALA533 4.7 25.2 1.0
H B:LEU530 4.7 18.1 1.0
CA B:GLY529 4.7 20.6 1.0
H B:ILE534 4.8 23.0 1.0
HB3 B:ALA533 4.8 32.7 1.0
C B:GLY529 4.8 12.5 1.0
N B:LEU530 4.9 14.9 1.0
HA B:CYS531 4.9 16.7 1.0
SG B:CYS512 5.0 16.0 1.0
HB3 B:CYS509 5.0 12.8 1.0
SG B:CYS509 5.0 18.1 1.0

Iron binding site 8 out of 8 in 7nz5

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Iron binding site 8 out of 8 in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:12.8
occ:1.00
FE4 B:SF4801 0.0 12.8 1.0
S1 B:SF4801 2.3 16.5 1.0
S2 B:SF4801 2.3 12.7 1.0
S3 B:SF4801 2.3 12.4 1.0
SG B:CYS512 2.5 16.0 1.0
FE1 B:SF4801 2.7 13.2 1.0
FE2 B:SF4801 2.7 14.6 1.0
FE3 B:SF4801 2.7 12.7 1.0
HB2 B:CYS512 3.2 13.8 1.0
CB B:CYS512 3.5 11.4 1.0
HD11 B:ILE149 3.6 27.0 1.0
H B:CYS512 3.7 14.0 1.0
ZN B:ZN802 3.8 6.3 0.5
HD12 B:ILE149 3.8 27.0 1.0
S4 B:SF4801 3.9 13.4 1.0
HB3 B:LEU511 3.9 18.0 1.0
HB3 B:CYS531 4.0 18.2 1.0
CD1 B:ILE149 4.1 22.4 1.0
HD13 B:ILE149 4.1 27.0 1.0
N B:CYS512 4.2 11.5 1.0
HB3 B:CYS512 4.2 13.8 1.0
SG B:CYS598 4.3 17.3 1.0
CA B:CYS512 4.4 12.7 1.0
HE2 B:HIS519 4.4 21.7 1.0
SG B:CYS600 4.5 15.3 1.0
HD23 B:LEU511 4.6 26.7 1.0
HG21 B:VAL152 4.6 19.8 1.0
HD2 B:HIS519 4.6 12.9 1.0
HA B:CYS512 4.7 15.3 1.0
O B:HOH1360 4.8 12.3 1.0
CB B:CYS531 4.8 15.1 1.0
CB B:LEU511 4.9 14.9 1.0
SG B:CYS531 4.9 18.1 1.0
H B:CYS531 4.9 14.7 1.0
H B:LEU511 4.9 12.7 1.0
SG B:CYS509 5.0 18.1 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 Aug 8 10:00:13 2024

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