Iron 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 Binding Sites:
The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron 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 Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7o0d
Go back to
Iron Binding Sites List in 7o0d
Iron binding site 1 out
of 4 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 Iron with other atoms in the Fe 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:Fe801
b:43.5
occ:1.00
|
FE1
|
A:SF4801
|
0.0
|
43.5
|
1.0
|
SG
|
A:CYS509
|
2.3
|
49.0
|
1.0
|
S2
|
A:SF4801
|
2.3
|
44.2
|
1.0
|
S3
|
A:SF4801
|
2.3
|
41.6
|
1.0
|
S4
|
A:SF4801
|
2.3
|
41.9
|
1.0
|
FE4
|
A:SF4801
|
2.7
|
44.7
|
1.0
|
FE2
|
A:SF4801
|
2.7
|
41.9
|
1.0
|
FE3
|
A:SF4801
|
2.7
|
40.4
|
1.0
|
HB3
|
A:CYS509
|
2.8
|
55.9
|
1.0
|
HD12
|
A:ILE534
|
2.9
|
73.2
|
1.0
|
CB
|
A:CYS509
|
3.1
|
46.4
|
1.0
|
HB2
|
A:LEU511
|
3.1
|
59.4
|
1.0
|
HB2
|
A:CYS509
|
3.6
|
55.9
|
1.0
|
H
|
A:LEU511
|
3.8
|
59.8
|
1.0
|
CD1
|
A:ILE534
|
3.8
|
60.9
|
1.0
|
S1
|
A:SF4801
|
3.9
|
41.6
|
1.0
|
HD12
|
A:LEU511
|
3.9
|
69.1
|
1.0
|
HB2
|
A:CYS521
|
3.9
|
49.1
|
1.0
|
HD11
|
A:ILE534
|
4.0
|
73.2
|
1.0
|
CB
|
A:LEU511
|
4.1
|
49.4
|
1.0
|
HD13
|
A:ILE534
|
4.2
|
73.2
|
1.0
|
HB3
|
A:LEU511
|
4.3
|
59.4
|
1.0
|
H
|
A:CYS512
|
4.4
|
52.0
|
1.0
|
CA
|
A:CYS509
|
4.4
|
39.2
|
1.0
|
N
|
A:LEU511
|
4.5
|
49.7
|
1.0
|
C
|
A:CYS509
|
4.5
|
48.6
|
1.0
|
HD13
|
A:LEU511
|
4.5
|
69.1
|
1.0
|
HB
|
A:ILE534
|
4.6
|
60.1
|
1.0
|
CD1
|
A:LEU511
|
4.6
|
57.4
|
1.0
|
SG
|
A:CYS512
|
4.6
|
46.3
|
1.0
|
CB
|
A:CYS521
|
4.6
|
40.8
|
1.0
|
O
|
A:CYS509
|
4.7
|
46.3
|
1.0
|
SG
|
A:CYS521
|
4.7
|
41.3
|
1.0
|
HG21
|
A:ILE534
|
4.7
|
58.5
|
1.0
|
HA
|
A:CYS509
|
4.7
|
47.2
|
1.0
|
HB3
|
A:CYS521
|
4.8
|
49.1
|
1.0
|
CA
|
A:LEU511
|
4.8
|
50.8
|
1.0
|
SG
|
A:CYS531
|
4.9
|
41.1
|
1.0
|
CG
|
A:LEU511
|
4.9
|
62.2
|
1.0
|
CG1
|
A:ILE534
|
4.9
|
56.0
|
1.0
|
N
|
A:CYS512
|
4.9
|
43.2
|
1.0
|
HB2
|
A:CYS512
|
5.0
|
55.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 7o0d
Go back to
Iron Binding Sites List in 7o0d
Iron binding site 2 out
of 4 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 Iron with other atoms in the Fe 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:Fe801
b:41.9
occ:1.00
|
FE2
|
A:SF4801
|
0.0
|
41.9
|
1.0
|
S4
|
A:SF4801
|
2.3
|
41.9
|
1.0
|
S1
|
A:SF4801
|
2.3
|
41.6
|
1.0
|
SG
|
A:CYS521
|
2.3
|
41.3
|
1.0
|
S3
|
A:SF4801
|
2.3
|
41.6
|
1.0
|
FE3
|
A:SF4801
|
2.7
|
40.4
|
1.0
|
FE1
|
A:SF4801
|
2.7
|
43.5
|
1.0
|
FE4
|
A:SF4801
|
2.7
|
44.7
|
1.0
|
HB2
|
A:CYS521
|
2.9
|
49.1
|
1.0
|
HE2
|
A:HIS519
|
3.1
|
52.5
|
1.0
|
CB
|
A:CYS521
|
3.2
|
40.8
|
1.0
|
HG
|
A:LEU530
|
3.5
|
51.5
|
1.0
|
HB3
|
A:CYS521
|
3.5
|
49.1
|
1.0
|
HB3
|
A:CYS509
|
3.5
|
55.9
|
1.0
|
S2
|
A:SF4801
|
3.9
|
44.2
|
1.0
|
H
|
A:LEU530
|
3.9
|
50.6
|
1.0
|
NE2
|
A:HIS519
|
3.9
|
43.7
|
1.0
|
H
|
A:CYS531
|
4.1
|
50.4
|
1.0
|
HA3
|
A:GLY529
|
4.3
|
53.8
|
1.0
|
CB
|
A:CYS509
|
4.4
|
46.4
|
1.0
|
CG
|
A:LEU530
|
4.4
|
42.8
|
1.0
|
HD11
|
A:LEU530
|
4.4
|
50.8
|
1.0
|
HA2
|
A:GLY529
|
4.5
|
53.8
|
1.0
|
HD21
|
A:LEU530
|
4.5
|
57.4
|
1.0
|
CA
|
A:CYS521
|
4.5
|
38.5
|
1.0
|
N
|
A:LEU530
|
4.5
|
42.0
|
1.0
|
SG
|
A:CYS509
|
4.6
|
49.0
|
1.0
|
HD2
|
A:HIS519
|
4.6
|
45.6
|
1.0
|
NI
|
A:NI802
|
4.6
|
51.1
|
1.0
|
H
|
A:CYS521
|
4.7
|
47.1
|
1.0
|
HB2
|
A:CYS509
|
4.7
|
55.9
|
1.0
|
CD2
|
A:HIS519
|
4.7
|
37.9
|
1.0
|
HD12
|
A:LEU530
|
4.7
|
50.8
|
1.0
|
SG
|
A:CYS598
|
4.7
|
40.3
|
1.0
|
HB2
|
A:CYS512
|
4.7
|
55.6
|
1.0
|
HB3
|
A:CYS531
|
4.7
|
54.2
|
1.0
|
CA
|
A:GLY529
|
4.8
|
44.7
|
1.0
|
CD1
|
A:LEU530
|
4.8
|
42.2
|
1.0
|
SG
|
A:CYS531
|
4.8
|
41.1
|
1.0
|
HA
|
A:CYS521
|
4.8
|
46.4
|
1.0
|
SG
|
A:CYS512
|
4.8
|
46.3
|
1.0
|
CD2
|
A:LEU530
|
4.9
|
47.7
|
1.0
|
N
|
A:CYS521
|
4.9
|
39.2
|
1.0
|
N
|
A:CYS531
|
5.0
|
41.9
|
1.0
|
CE1
|
A:HIS519
|
5.0
|
39.9
|
1.0
|
HD12
|
A:ILE534
|
5.0
|
73.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 7o0d
Go back to
Iron Binding Sites List in 7o0d
Iron binding site 3 out
of 4 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 Iron with other atoms in the Fe binding
site number 3 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:Fe801
b:40.4
occ:1.00
|
FE3
|
A:SF4801
|
0.0
|
40.4
|
1.0
|
S4
|
A:SF4801
|
2.3
|
41.9
|
1.0
|
SG
|
A:CYS531
|
2.3
|
41.1
|
1.0
|
S1
|
A:SF4801
|
2.3
|
41.6
|
1.0
|
S2
|
A:SF4801
|
2.3
|
44.2
|
1.0
|
FE2
|
A:SF4801
|
2.7
|
41.9
|
1.0
|
FE1
|
A:SF4801
|
2.7
|
43.5
|
1.0
|
FE4
|
A:SF4801
|
2.7
|
44.7
|
1.0
|
HB3
|
A:CYS531
|
2.9
|
54.2
|
1.0
|
H
|
A:CYS531
|
3.2
|
50.4
|
1.0
|
CB
|
A:CYS531
|
3.2
|
45.1
|
1.0
|
HD12
|
A:ILE534
|
3.5
|
73.2
|
1.0
|
HB2
|
A:CYS531
|
3.9
|
54.2
|
1.0
|
HB
|
A:ILE534
|
3.9
|
60.1
|
1.0
|
S3
|
A:SF4801
|
3.9
|
41.6
|
1.0
|
HA3
|
A:GLY529
|
3.9
|
53.8
|
1.0
|
N
|
A:CYS531
|
3.9
|
41.9
|
1.0
|
CA
|
A:CYS531
|
4.2
|
46.7
|
1.0
|
HG13
|
A:ILE534
|
4.2
|
67.3
|
1.0
|
CD1
|
A:ILE534
|
4.3
|
60.9
|
1.0
|
HD11
|
A:ILE534
|
4.4
|
73.2
|
1.0
|
NI
|
A:NI802
|
4.4
|
51.1
|
1.0
|
H
|
A:LEU530
|
4.6
|
50.6
|
1.0
|
CG1
|
A:ILE534
|
4.6
|
56.0
|
1.0
|
HG
|
A:LEU530
|
4.6
|
51.5
|
1.0
|
CA
|
A:GLY529
|
4.7
|
44.7
|
1.0
|
CB
|
A:ILE534
|
4.7
|
50.0
|
1.0
|
C
|
A:GLY529
|
4.7
|
41.3
|
1.0
|
N
|
A:LEU530
|
4.7
|
42.0
|
1.0
|
S
|
A:MEE804
|
4.7
|
68.4
|
1.0
|
H
|
A:ALA533
|
4.8
|
60.3
|
1.0
|
HD12
|
A:LEU530
|
4.8
|
50.8
|
1.0
|
SG
|
A:CYS521
|
4.8
|
41.3
|
1.0
|
SG
|
A:CYS509
|
4.8
|
49.0
|
1.0
|
SG
|
A:CYS512
|
4.8
|
46.3
|
1.0
|
H
|
A:GLY532
|
4.8
|
56.4
|
1.0
|
HA
|
A:CYS531
|
4.8
|
56.1
|
1.0
|
HA2
|
A:GLY529
|
4.9
|
53.8
|
1.0
|
H
|
A:ILE534
|
4.9
|
61.3
|
1.0
|
SG
|
A:CYS600
|
5.0
|
43.2
|
1.0
|
HB3
|
A:CYS509
|
5.0
|
55.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 7o0d
Go back to
Iron Binding Sites List in 7o0d
Iron binding site 4 out
of 4 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 Iron with other atoms in the Fe binding
site number 4 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:Fe801
b:44.7
occ:1.00
|
FE4
|
A:SF4801
|
0.0
|
44.7
|
1.0
|
SG
|
A:CYS512
|
2.3
|
46.3
|
1.0
|
S3
|
A:SF4801
|
2.3
|
41.6
|
1.0
|
S2
|
A:SF4801
|
2.3
|
44.2
|
1.0
|
S1
|
A:SF4801
|
2.3
|
41.6
|
1.0
|
NI
|
A:NI802
|
2.6
|
51.1
|
1.0
|
FE1
|
A:SF4801
|
2.7
|
43.5
|
1.0
|
FE2
|
A:SF4801
|
2.7
|
41.9
|
1.0
|
FE3
|
A:SF4801
|
2.7
|
40.4
|
1.0
|
HB2
|
A:CYS512
|
3.2
|
55.6
|
1.0
|
CB
|
A:CYS512
|
3.4
|
46.2
|
1.0
|
S
|
A:MEE804
|
3.7
|
68.4
|
1.0
|
SG
|
A:CYS598
|
3.8
|
40.3
|
1.0
|
H
|
A:CYS512
|
3.8
|
52.0
|
1.0
|
S4
|
A:SF4801
|
3.9
|
41.9
|
1.0
|
HB3
|
A:CYS531
|
3.9
|
54.2
|
1.0
|
H1
|
A:MEE804
|
4.1
|
74.1
|
1.0
|
HB3
|
A:CYS512
|
4.1
|
55.6
|
1.0
|
N
|
A:CYS512
|
4.2
|
43.2
|
1.0
|
HB2
|
A:LEU511
|
4.2
|
59.4
|
1.0
|
CA
|
A:CYS512
|
4.4
|
35.3
|
1.0
|
SG
|
A:CYS600
|
4.4
|
43.2
|
1.0
|
C
|
A:MEE804
|
4.4
|
61.6
|
1.0
|
HE2
|
A:HIS519
|
4.5
|
52.5
|
1.0
|
HB3
|
A:LEU511
|
4.5
|
59.4
|
1.0
|
H3
|
A:MEE804
|
4.6
|
74.1
|
1.0
|
SG
|
A:CYS531
|
4.7
|
41.1
|
1.0
|
HA
|
A:CYS512
|
4.7
|
42.5
|
1.0
|
HD2
|
A:HIS519
|
4.7
|
45.6
|
1.0
|
CB
|
A:CYS531
|
4.7
|
45.1
|
1.0
|
CB
|
A:LEU511
|
4.8
|
49.4
|
1.0
|
HD11
|
A:LEU530
|
4.8
|
50.8
|
1.0
|
SG
|
A:CYS509
|
4.8
|
49.0
|
1.0
|
SG
|
A:CYS521
|
4.8
|
41.3
|
1.0
|
H
|
A:CYS531
|
4.8
|
50.4
|
1.0
|
HB3
|
A:CYS509
|
4.9
|
55.9
|
1.0
|
C
|
A:LEU511
|
4.9
|
53.3
|
1.0
|
H
|
A:LEU511
|
5.0
|
59.8
|
1.0
|
HB3
|
A:CYS598
|
5.0
|
42.8
|
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 Aug 8 10:00:15 2024
|