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Iron 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
Nickel (Ni) 4 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 7nys

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Iron binding site 1 out of 8 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 Iron with other atoms in the Fe 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:Fe801

b:22.8
occ:1.00
FE1 A:SF4801 0.0 22.8 1.0
SG A:CYS509 2.2 28.3 1.0
S3 A:SF4801 2.3 23.2 1.0
S2 A:SF4801 2.3 26.4 1.0
S4 A:SF4801 2.3 25.1 1.0
FE2 A:SF4801 2.7 21.5 1.0
FE4 A:SF4801 2.7 23.4 1.0
FE3 A:SF4801 2.7 22.6 1.0
HB3 A:CYS509 2.8 26.9 1.0
CB A:CYS509 3.1 22.4 1.0
HB3 A:LEU511 3.4 30.1 1.0
HB2 A:CYS509 3.6 26.9 1.0
HG13 A:ILE534 3.7 31.0 1.0
H A:LEU511 3.8 28.9 1.0
S1 A:SF4801 3.9 25.4 1.0
HB2 A:CYS521 4.0 28.8 1.0
CB A:LEU511 4.2 25.1 1.0
HB2 A:LEU511 4.3 30.1 1.0
H A:CYS512 4.3 23.3 1.0
HD23 A:LEU511 4.3 34.4 1.0
CA A:CYS509 4.4 26.4 1.0
HB A:ILE534 4.4 23.7 1.0
C A:CYS509 4.4 28.4 1.0
CG1 A:ILE534 4.4 25.9 1.0
HG12 A:ILE534 4.4 31.0 1.0
N A:LEU511 4.5 24.1 1.0
O A:CYS509 4.5 23.9 1.0
HG21 A:ILE534 4.5 23.1 1.0
SG A:CYS521 4.7 25.1 1.0
CB A:CYS521 4.7 24.0 1.0
HD21 A:ASN551 4.7 34.2 1.0
HD22 A:LEU511 4.7 34.4 1.0
HB3 A:CYS521 4.8 28.8 1.0
SG A:CYS512 4.8 26.2 1.0
HA A:CYS509 4.8 31.7 1.0
CB A:ILE534 4.9 19.7 1.0
CD2 A:LEU511 4.9 28.7 1.0
HB2 A:CYS512 4.9 28.6 1.0
CA A:LEU511 4.9 23.3 1.0
SG A:CYS531 5.0 24.6 1.0
N A:CYS512 5.0 19.4 1.0
N A:LEU510 5.0 26.5 1.0

Iron binding site 2 out of 8 in 7nys

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Iron binding site 2 out of 8 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 Iron with other atoms in the Fe 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:Fe801

b:21.5
occ:1.00
FE2 A:SF4801 0.0 21.5 1.0
SG A:CYS521 2.2 25.1 1.0
S1 A:SF4801 2.3 25.4 1.0
S4 A:SF4801 2.3 25.1 1.0
S3 A:SF4801 2.3 23.2 1.0
FE3 A:SF4801 2.7 22.6 1.0
FE1 A:SF4801 2.7 22.8 1.0
FE4 A:SF4801 2.7 23.4 1.0
HB2 A:CYS521 2.9 28.8 1.0
CB A:CYS521 3.1 24.0 1.0
HE2 A:HIS519 3.3 37.2 1.0
HB3 A:CYS521 3.4 28.8 1.0
HG A:LEU530 3.5 24.7 1.0
HB3 A:CYS509 3.6 26.9 1.0
S2 A:SF4801 3.9 26.4 1.0
H A:LEU530 4.0 26.1 1.0
NE2 A:HIS519 4.1 31.0 1.0
H A:CYS531 4.1 25.4 1.0
HA3 A:GLY529 4.2 25.6 1.0
CG A:LEU530 4.4 20.6 1.0
CB A:CYS509 4.5 22.4 1.0
SG A:CYS509 4.5 28.3 1.0
CA A:CYS521 4.6 20.6 1.0
N A:LEU530 4.6 21.8 1.0
HB3 A:CYS531 4.6 27.2 1.0
HD21 A:LEU530 4.6 30.7 1.0
HD11 A:LEU530 4.6 31.0 1.0
HA2 A:GLY529 4.7 25.6 1.0
HD23 A:LEU530 4.7 30.7 1.0
HD2 A:HIS519 4.7 25.9 1.0
HB2 A:CYS512 4.7 28.6 1.0
H A:CYS521 4.8 29.1 1.0
CA A:GLY529 4.8 21.3 1.0
O A:CYS509 4.8 23.9 1.0
CD2 A:LEU530 4.8 25.6 1.0
CD2 A:HIS519 4.9 21.6 1.0
HA A:CYS521 4.9 24.7 1.0
SG A:CYS531 4.9 24.6 1.0
HB2 A:CYS509 4.9 26.9 1.0
O A:HOH1285 4.9 27.9 1.0
SG A:CYS512 4.9 26.2 1.0
N A:CYS531 5.0 21.1 1.0
CD1 A:LEU530 5.0 25.8 1.0

Iron binding site 3 out of 8 in 7nys

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Iron binding site 3 out of 8 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 Iron with other atoms in the Fe 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
A:Fe801

b:22.6
occ:1.00
FE3 A:SF4801 0.0 22.6 1.0
S1 A:SF4801 2.3 25.4 1.0
S4 A:SF4801 2.3 25.1 1.0
S2 A:SF4801 2.3 26.4 1.0
SG A:CYS531 2.4 24.6 1.0
FE2 A:SF4801 2.7 21.5 1.0
FE4 A:SF4801 2.7 23.4 1.0
FE1 A:SF4801 2.7 22.8 1.0
HB3 A:CYS531 2.7 27.2 1.0
CB A:CYS531 3.1 22.7 1.0
H A:CYS531 3.2 25.4 1.0
HD11 A:ILE149 3.7 44.2 1.0
HG12 A:ILE534 3.7 31.0 1.0
HB2 A:CYS531 3.8 27.2 1.0
S3 A:SF4801 3.9 23.2 1.0
HB A:ILE534 3.9 23.7 1.0
N A:CYS531 3.9 21.1 1.0
HG13 A:ILE534 4.0 31.0 1.0
HA3 A:GLY529 4.1 25.6 1.0
CA A:CYS531 4.1 22.2 1.0
CG1 A:ILE534 4.2 25.9 1.0
HG A:LEU530 4.5 24.7 1.0
CD1 A:ILE149 4.6 36.8 1.0
CB A:ILE534 4.6 19.7 1.0
H A:LEU530 4.7 26.1 1.0
HD13 A:ILE149 4.7 44.2 1.0
SG A:CYS509 4.7 28.3 1.0
SG A:CYS521 4.7 25.1 1.0
H A:ALA533 4.7 34.5 1.0
H A:ILE534 4.8 28.2 1.0
N A:LEU530 4.8 21.8 1.0
HA A:CYS531 4.8 26.7 1.0
C A:GLY529 4.8 24.4 1.0
H A:GLY532 4.8 30.0 1.0
SG A:CYS512 4.9 26.2 1.0
CA A:GLY529 4.9 21.3 1.0
HB3 A:CYS509 5.0 26.9 1.0

Iron binding site 4 out of 8 in 7nys

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Iron binding site 4 out of 8 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 Iron with other atoms in the Fe 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
A:Fe801

b:23.4
occ:1.00
FE4 A:SF4801 0.0 23.4 1.0
S3 A:SF4801 2.3 23.2 1.0
S1 A:SF4801 2.3 25.4 1.0
S2 A:SF4801 2.3 26.4 1.0
SG A:CYS512 2.4 26.2 1.0
FE1 A:SF4801 2.7 22.8 1.0
FE2 A:SF4801 2.7 21.5 1.0
FE3 A:SF4801 2.7 22.6 1.0
HB2 A:CYS512 3.1 28.6 1.0
HD11 A:ILE149 3.3 44.2 1.0
CB A:CYS512 3.4 23.8 1.0
H A:CYS512 3.7 23.3 1.0
S4 A:SF4801 3.9 25.1 1.0
NI A:UWE802 3.9 23.6 1.0
HB3 A:LEU511 3.9 30.1 1.0
HB3 A:CYS531 4.0 27.2 1.0
HB3 A:CYS512 4.0 28.6 1.0
HD12 A:ILE149 4.0 44.2 1.0
CD1 A:ILE149 4.1 36.8 1.0
N A:CYS512 4.2 19.4 1.0
SG A:CYS600 4.2 24.0 1.0
SG A:CYS598 4.3 24.2 1.0
HD13 A:ILE149 4.3 44.2 1.0
HD23 A:LEU511 4.4 34.4 1.0
CA A:CYS512 4.4 29.0 1.0
HE2 A:HIS519 4.5 37.2 1.0
HD2 A:HIS519 4.6 25.9 1.0
SG A:CYS521 4.7 25.1 1.0
HA A:CYS512 4.7 34.8 1.0
SG A:CYS509 4.8 28.3 1.0
CB A:CYS531 4.8 22.7 1.0
HG21 A:VAL152 4.8 34.1 1.0
SG A:CYS531 4.8 24.6 1.0
CB A:LEU511 4.9 25.1 1.0
H A:LEU511 4.9 28.9 1.0
O A:HOH1420 4.9 25.8 1.0
HD11 A:LEU530 5.0 31.0 1.0
HB2 A:CYS521 5.0 28.8 1.0

Iron binding site 5 out of 8 in 7nys

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Iron binding site 5 out of 8 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 Iron with other atoms in the Fe binding site number 5 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:Fe801

b:18.8
occ:1.00
FE1 B:SF4801 0.0 18.8 1.0
S2 B:SF4801 2.3 17.0 1.0
S3 B:SF4801 2.3 17.9 1.0
S4 B:SF4801 2.3 18.4 1.0
SG B:CYS509 2.3 20.2 1.0
FE2 B:SF4801 2.7 20.3 1.0
FE4 B:SF4801 2.7 21.2 1.0
FE3 B:SF4801 2.7 19.3 1.0
HB3 B:CYS509 2.8 23.4 1.0
CB B:CYS509 3.1 19.5 1.0
HB3 B:LEU511 3.4 19.2 1.0
HG13 B:ILE534 3.6 28.0 1.0
HB2 B:CYS509 3.7 23.4 1.0
H B:LEU511 3.7 19.6 1.0
S1 B:SF4801 3.9 19.6 1.0
HB2 B:CYS521 4.0 29.9 1.0
HB2 B:LEU511 4.2 19.2 1.0
CB B:LEU511 4.2 16.0 1.0
HD23 B:LEU511 4.3 33.2 1.0
H B:CYS512 4.3 21.8 1.0
CA B:CYS509 4.3 18.7 1.0
C B:CYS509 4.4 23.2 1.0
N B:LEU511 4.5 16.4 1.0
HB B:ILE534 4.5 27.8 1.0
CG1 B:ILE534 4.5 23.4 1.0
O B:CYS509 4.5 18.6 1.0
HG21 B:ILE534 4.6 26.6 1.0
SG B:CYS521 4.6 18.9 1.0
CB B:CYS521 4.7 24.9 1.0
SG B:CYS512 4.8 19.9 1.0
HB3 B:CYS521 4.8 29.9 1.0
HA B:CYS509 4.8 22.4 1.0
HG12 B:ILE534 4.8 28.0 1.0
HD21 B:ASN551 4.8 28.5 1.0
HB2 B:CYS512 4.9 19.0 1.0
CA B:LEU511 4.9 21.9 1.0
CB B:ILE534 4.9 23.1 1.0
N B:CYS512 4.9 18.2 1.0
SG B:CYS531 5.0 19.0 1.0
N B:LEU510 5.0 21.8 1.0

Iron binding site 6 out of 8 in 7nys

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Iron binding site 6 out of 8 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 Iron with other atoms in the Fe binding site number 6 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:Fe801

b:20.3
occ:1.00
FE2 B:SF4801 0.0 20.3 1.0
SG B:CYS521 2.2 18.9 1.0
S3 B:SF4801 2.3 17.9 1.0
S1 B:SF4801 2.3 19.6 1.0
S4 B:SF4801 2.3 18.4 1.0
FE1 B:SF4801 2.7 18.8 1.0
FE4 B:SF4801 2.7 21.2 1.0
FE3 B:SF4801 2.7 19.3 1.0
HB2 B:CYS521 2.9 29.9 1.0
CB B:CYS521 3.1 24.9 1.0
HE2 B:HIS519 3.2 27.2 1.0
HB3 B:CYS521 3.4 29.9 1.0
HG B:LEU530 3.5 24.3 1.0
HB3 B:CYS509 3.6 23.4 1.0
S2 B:SF4801 3.9 17.0 1.0
H B:LEU530 4.0 19.9 1.0
NE2 B:HIS519 4.0 22.7 1.0
H B:CYS531 4.2 25.7 1.0
HA3 B:GLY529 4.2 26.1 1.0
CG B:LEU530 4.4 20.2 1.0
HD21 B:LEU530 4.5 23.9 1.0
CB B:CYS509 4.5 19.5 1.0
CA B:CYS521 4.6 18.6 1.0
N B:LEU530 4.6 16.6 1.0
HA2 B:GLY529 4.7 26.1 1.0
SG B:CYS509 4.7 20.2 1.0
HB3 B:CYS531 4.7 24.6 1.0
O B:HOH1255 4.7 21.8 1.0
HD2 B:HIS519 4.7 19.6 1.0
H B:CYS521 4.7 21.5 1.0
HD23 B:LEU530 4.7 23.9 1.0
HD11 B:LEU530 4.7 26.2 1.0
HB2 B:CYS512 4.8 19.0 1.0
CD2 B:LEU530 4.8 19.9 1.0
CD2 B:HIS519 4.8 16.3 1.0
CA B:GLY529 4.8 21.8 1.0
HA B:CYS521 4.9 22.3 1.0
SG B:CYS531 4.9 19.0 1.0
O B:CYS509 4.9 18.6 1.0
N B:CYS531 4.9 21.4 1.0
HB2 B:CYS509 5.0 23.4 1.0
N B:CYS521 5.0 17.9 1.0
SG B:CYS512 5.0 19.9 1.0

Iron binding site 7 out of 8 in 7nys

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Iron binding site 7 out of 8 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 Iron with other atoms in the Fe binding site number 7 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:Fe801

b:19.3
occ:1.00
FE3 B:SF4801 0.0 19.3 1.0
S4 B:SF4801 2.3 18.4 1.0
S2 B:SF4801 2.3 17.0 1.0
S1 B:SF4801 2.3 19.6 1.0
SG B:CYS531 2.4 19.0 1.0
FE1 B:SF4801 2.7 18.8 1.0
FE2 B:SF4801 2.7 20.3 1.0
FE4 B:SF4801 2.7 21.2 1.0
HB3 B:CYS531 2.7 24.6 1.0
H B:CYS531 3.1 25.7 1.0
CB B:CYS531 3.1 20.5 1.0
HD11 B:ILE149 3.6 34.2 1.0
HG13 B:ILE534 3.7 28.0 1.0
HB2 B:CYS531 3.8 24.6 1.0
N B:CYS531 3.9 21.4 1.0
S3 B:SF4801 3.9 17.9 1.0
HG12 B:ILE534 3.9 28.0 1.0
HB B:ILE534 4.0 27.8 1.0
HA3 B:GLY529 4.0 26.1 1.0
CA B:CYS531 4.1 18.0 1.0
CG1 B:ILE534 4.2 23.4 1.0
HD13 B:ILE149 4.3 34.2 1.0
CD1 B:ILE149 4.4 28.5 1.0
O B:HOH1678 4.4 39.5 1.0
HG B:LEU530 4.5 24.3 1.0
CB B:ILE534 4.6 23.1 1.0
H B:LEU530 4.7 19.9 1.0
HD12 B:ILE149 4.7 34.2 1.0
SG B:CYS521 4.8 18.9 1.0
HA B:CYS531 4.8 21.6 1.0
N B:LEU530 4.8 16.6 1.0
H B:ALA533 4.8 29.3 1.0
H B:ILE534 4.8 26.9 1.0
C B:GLY529 4.8 17.9 1.0
CA B:GLY529 4.8 21.8 1.0
SG B:CYS509 4.8 20.2 1.0
SG B:CYS512 4.9 19.9 1.0
H B:GLY532 5.0 25.4 1.0
HB3 B:CYS509 5.0 23.4 1.0

Iron binding site 8 out of 8 in 7nys

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Iron binding site 8 out of 8 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 Iron with other atoms in the Fe binding site number 8 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:Fe801

b:21.2
occ:1.00
FE4 B:SF4801 0.0 21.2 1.0
S1 B:SF4801 2.3 19.6 1.0
S3 B:SF4801 2.3 17.9 1.0
S2 B:SF4801 2.3 17.0 1.0
SG B:CYS512 2.4 19.9 1.0
FE2 B:SF4801 2.7 20.3 1.0
FE1 B:SF4801 2.7 18.8 1.0
FE3 B:SF4801 2.7 19.3 1.0
HB2 B:CYS512 3.1 19.0 1.0
CB B:CYS512 3.4 15.8 1.0
H B:CYS512 3.7 21.8 1.0
HD11 B:ILE149 3.8 34.2 1.0
NI B:UWE802 3.8 20.2 1.0
S4 B:SF4801 3.9 18.4 1.0
HB3 B:LEU511 3.9 19.2 1.0
HD12 B:ILE149 4.0 34.2 1.0
HB3 B:CYS531 4.1 24.6 1.0
HB3 B:CYS512 4.1 19.0 1.0
N B:CYS512 4.2 18.2 1.0
CD1 B:ILE149 4.2 28.5 1.0
SG B:CYS598 4.3 17.8 1.0
HD13 B:ILE149 4.4 34.2 1.0
HE2 B:HIS519 4.4 27.2 1.0
CA B:CYS512 4.4 17.3 1.0
SG B:CYS600 4.4 20.4 1.0
HD2 B:HIS519 4.7 19.6 1.0
HA B:CYS512 4.7 20.8 1.0
SG B:CYS521 4.7 18.9 1.0
HD23 B:LEU511 4.7 33.2 1.0
HG21 B:VAL152 4.7 27.7 1.0
SG B:CYS509 4.9 20.2 1.0
CB B:CYS531 4.9 20.5 1.0
CB B:LEU511 4.9 16.0 1.0
H B:LEU511 4.9 19.6 1.0
SG B:CYS531 4.9 19.0 1.0
O B:HOH1345 4.9 16.7 1.0
HG B:LEU530 5.0 24.3 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 09:57:48 2024

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