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:
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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