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Nickel in PDB 7o0d: Monomeric Acetyl-Coa Synthase in Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal

Enzymatic activity of Monomeric Acetyl-Coa Synthase in Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal

All present enzymatic activity of Monomeric Acetyl-Coa Synthase in Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal:
2.3.1.169;

Protein crystallography data

The structure of Monomeric Acetyl-Coa Synthase in Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal, PDB code: 7o0d 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) 48.88 / 2.30
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 199.344, 199.344, 168.268, 90, 90, 120
R / Rfree (%) 19.6 / 22.2

Other elements in 7o0d:

The structure of Monomeric Acetyl-Coa Synthase in Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Monomeric Acetyl-Coa Synthase in Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal (pdb code 7o0d). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Monomeric Acetyl-Coa Synthase in Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal, PDB code: 7o0d:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 7o0d

Go back to Nickel Binding Sites List in 7o0d
Nickel binding site 1 out of 2 in the Monomeric Acetyl-Coa Synthase in Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal


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 Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni802

b:51.1
occ:1.00
SG A:CYS512 2.1 46.3 1.0
SG A:CYS600 2.3 43.2 1.0
SG A:CYS598 2.3 40.3 1.0
S A:MEE804 2.4 68.4 1.0
FE4 A:SF4801 2.6 44.7 1.0
NI A:NI803 2.9 39.6 1.0
S1 A:SF4801 3.0 41.6 1.0
HZ A:PHE515 3.3 63.6 1.0
HB3 A:CYS600 3.3 55.7 1.0
CB A:CYS512 3.4 46.2 1.0
HB3 A:CYS512 3.4 55.6 1.0
CB A:CYS600 3.5 46.3 1.0
HB2 A:CYS598 3.6 42.8 1.0
HB2 A:CYS512 3.6 55.6 1.0
CB A:CYS598 3.7 35.5 1.0
HB3 A:CYS531 3.7 54.2 1.0
C A:MEE804 3.7 61.6 1.0
H3 A:MEE804 3.8 74.1 1.0
HD11 A:LEU530 3.9 50.8 1.0
H1 A:MEE804 4.0 74.1 1.0
HB3 A:CYS598 4.0 42.8 1.0
HB2 A:CYS600 4.1 55.7 1.0
CZ A:PHE515 4.1 52.9 1.0
HE1 A:PHE515 4.1 65.3 1.0
HD12 A:LEU530 4.3 50.8 1.0
S2 A:SF4801 4.3 44.2 1.0
N A:CYS600 4.3 39.0 1.0
FE3 A:SF4801 4.4 40.4 1.0
H2 A:MEE804 4.5 74.1 1.0
CE1 A:PHE515 4.5 54.3 1.0
CD1 A:LEU530 4.5 42.2 1.0
CA A:CYS600 4.5 47.0 1.0
S3 A:SF4801 4.5 41.6 1.0
CB A:CYS531 4.6 45.1 1.0
FE2 A:SF4801 4.6 41.9 1.0
N A:GLY599 4.6 31.7 1.0
CA A:CYS512 4.7 35.3 1.0
HA A:CYS512 4.7 42.5 1.0
H A:CYS598 4.7 52.0 1.0
CA A:CYS598 4.9 37.4 1.0
HB2 A:CYS531 5.0 54.2 1.0

Nickel binding site 2 out of 2 in 7o0d

Go back to Nickel Binding Sites List in 7o0d
Nickel binding site 2 out of 2 in the Monomeric Acetyl-Coa Synthase in Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal


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 Open Conformation with Methanethiol Moiety of Coa Bound to Nickel Proximal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni803

b:39.6
occ:1.00
N A:GLY599 2.0 31.7 1.0
N A:CYS600 2.0 39.0 1.0
SG A:CYS598 2.2 40.3 1.0
SG A:CYS600 2.4 43.2 1.0
C A:GLY599 2.8 41.5 1.0
NI A:NI802 2.9 51.1 1.0
CA A:GLY599 2.9 42.5 1.0
HB2 A:CYS598 3.0 42.8 1.0
CB A:CYS598 3.0 35.5 1.0
C A:CYS598 3.1 44.6 1.0
CA A:CYS600 3.1 47.0 1.0
CB A:CYS600 3.1 46.3 1.0
HD11 A:LEU530 3.1 50.8 1.0
HZ A:PHE515 3.2 63.6 1.0
HB3 A:CYS600 3.2 55.7 1.0
H A:CYS598 3.2 52.0 1.0
CA A:CYS598 3.4 37.4 1.0
H A:PHE601 3.4 51.0 1.0
HA3 A:GLY599 3.5 51.1 1.0
HA2 A:GLY599 3.5 51.1 1.0
N A:CYS598 3.7 43.2 1.0
C A:CYS600 3.7 48.3 1.0
N A:PHE601 3.7 42.4 1.0
CD1 A:LEU530 3.8 42.2 1.0
HD13 A:LEU530 3.8 50.8 1.0
HD12 A:LEU530 3.9 50.8 1.0
HB3 A:CYS598 3.9 42.8 1.0
HA A:CYS600 3.9 56.5 1.0
O A:GLY599 4.0 49.4 1.0
HE2 A:PHE515 4.0 63.0 1.0
CZ A:PHE515 4.0 52.9 1.0
HB2 A:CYS600 4.0 55.7 1.0
O A:CYS598 4.2 42.1 1.0
HA A:CYS598 4.3 45.0 1.0
CE2 A:PHE515 4.5 52.4 1.0
H61 A:PG4806 4.5 88.0 1.0
S A:MEE804 4.6 68.4 1.0
S1 A:SF4801 4.6 41.6 1.0
O A:CYS600 4.6 44.4 1.0
SG A:CYS512 4.7 46.3 1.0
HB3 A:CYS512 4.7 55.6 1.0
HB3 A:SER597 4.7 46.5 1.0
CA A:PHE601 4.8 44.9 1.0
HB3 A:PHE601 4.8 52.1 1.0
HA A:PHE601 4.9 54.0 1.0
C A:SER597 4.9 44.6 1.0
HD2 A:PHE601 4.9 53.0 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 09:18:55 2024

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