Zinc in PDB 3git: Crystal Structure of A Truncated Acetyl-Coa Synthase
Enzymatic activity of Crystal Structure of A Truncated Acetyl-Coa Synthase
All present enzymatic activity of Crystal Structure of A Truncated Acetyl-Coa Synthase:
2.3.1.169;
Protein crystallography data
The structure of Crystal Structure of A Truncated Acetyl-Coa Synthase, PDB code: 3git
was solved by
A.Volbeda,
C.Darnault,
J.C.Fontecilla-Camps,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.98 /
3.00
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
166.400,
166.400,
245.200,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.1 /
20.8
|
Other elements in 3git:
The structure of Crystal Structure of A Truncated Acetyl-Coa Synthase also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of A Truncated Acetyl-Coa Synthase
(pdb code 3git). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of A Truncated Acetyl-Coa Synthase, PDB code: 3git:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 3git
Go back to
Zinc Binding Sites List in 3git
Zinc binding site 1 out
of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn739
b:58.0
occ:0.75
|
SG
|
A:CYS597
|
2.2
|
57.8
|
1.0
|
S
|
A:H2S740
|
2.2
|
60.4
|
0.8
|
SG
|
A:CYS509
|
2.3
|
55.6
|
1.0
|
SG
|
A:CYS595
|
2.3
|
56.6
|
1.0
|
CB
|
A:CYS509
|
3.0
|
55.4
|
1.0
|
CB
|
A:CYS595
|
3.4
|
57.3
|
1.0
|
CB
|
A:CYS597
|
3.5
|
58.0
|
1.0
|
FE4
|
A:SF4738
|
3.5
|
56.0
|
1.0
|
N
|
A:CYS597
|
3.6
|
58.2
|
1.0
|
S1
|
A:SF4738
|
3.8
|
57.1
|
1.0
|
N
|
A:GLY596
|
4.0
|
59.3
|
1.0
|
CA
|
A:CYS597
|
4.1
|
58.0
|
1.0
|
NH2
|
A:ARG405
|
4.2
|
54.8
|
1.0
|
CA
|
A:CYS509
|
4.4
|
55.5
|
1.0
|
C
|
A:GLY596
|
4.5
|
58.9
|
1.0
|
CD2
|
A:LEU527
|
4.6
|
53.6
|
1.0
|
CA
|
A:CYS595
|
4.7
|
58.1
|
1.0
|
CA
|
A:GLY596
|
4.8
|
58.7
|
1.0
|
C
|
A:CYS595
|
4.8
|
58.8
|
1.0
|
C
|
A:CYS597
|
5.0
|
57.5
|
1.0
|
|
Zinc binding site 2 out
of 6 in 3git
Go back to
Zinc Binding Sites List in 3git
Zinc binding site 2 out
of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn739
b:57.4
occ:0.75
|
S
|
B:H2S740
|
2.2
|
57.7
|
0.8
|
SG
|
B:CYS595
|
2.3
|
57.9
|
1.0
|
SG
|
B:CYS597
|
2.3
|
58.5
|
1.0
|
SG
|
B:CYS509
|
2.3
|
54.4
|
1.0
|
CB
|
B:CYS509
|
3.1
|
54.9
|
1.0
|
CB
|
B:CYS595
|
3.4
|
57.9
|
1.0
|
N
|
B:CYS597
|
3.5
|
57.8
|
1.0
|
CB
|
B:CYS597
|
3.5
|
58.0
|
1.0
|
FE4
|
B:SF4738
|
3.6
|
55.8
|
1.0
|
S1
|
B:SF4738
|
3.8
|
54.5
|
1.0
|
N
|
B:GLY596
|
3.9
|
58.7
|
1.0
|
CA
|
B:CYS597
|
4.0
|
58.0
|
1.0
|
C
|
B:GLY596
|
4.4
|
58.2
|
1.0
|
NH2
|
B:ARG405
|
4.4
|
54.0
|
1.0
|
CA
|
B:CYS509
|
4.5
|
55.0
|
1.0
|
CD2
|
B:LEU527
|
4.5
|
53.7
|
1.0
|
CA
|
B:CYS595
|
4.6
|
58.3
|
1.0
|
CA
|
B:GLY596
|
4.6
|
58.2
|
1.0
|
C
|
B:CYS595
|
4.7
|
58.9
|
1.0
|
C
|
B:CYS597
|
4.8
|
57.7
|
1.0
|
|
Zinc binding site 3 out
of 6 in 3git
Go back to
Zinc Binding Sites List in 3git
Zinc binding site 3 out
of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn739
b:57.9
occ:0.75
|
SG
|
C:CYS595
|
2.2
|
57.8
|
1.0
|
S
|
C:H2S740
|
2.2
|
58.5
|
0.8
|
SG
|
C:CYS509
|
2.3
|
56.2
|
1.0
|
SG
|
C:CYS597
|
2.4
|
57.3
|
1.0
|
CB
|
C:CYS509
|
3.0
|
55.7
|
1.0
|
CB
|
C:CYS595
|
3.3
|
58.5
|
1.0
|
N
|
C:CYS597
|
3.6
|
58.0
|
1.0
|
FE4
|
C:SF4738
|
3.6
|
55.9
|
1.0
|
CB
|
C:CYS597
|
3.6
|
57.5
|
1.0
|
S1
|
C:SF4738
|
3.8
|
55.3
|
1.0
|
N
|
C:GLY596
|
3.9
|
58.9
|
1.0
|
CA
|
C:CYS597
|
4.1
|
57.9
|
1.0
|
CD2
|
C:LEU527
|
4.4
|
53.0
|
1.0
|
CA
|
C:CYS509
|
4.4
|
55.8
|
1.0
|
C
|
C:GLY596
|
4.4
|
58.3
|
1.0
|
NH2
|
C:ARG405
|
4.5
|
54.5
|
1.0
|
CA
|
C:CYS595
|
4.6
|
58.5
|
1.0
|
CA
|
C:GLY596
|
4.6
|
58.5
|
1.0
|
C
|
C:CYS595
|
4.7
|
58.8
|
1.0
|
C
|
C:CYS597
|
4.9
|
57.8
|
1.0
|
S2
|
C:SF4738
|
4.9
|
57.4
|
1.0
|
|
Zinc binding site 4 out
of 6 in 3git
Go back to
Zinc Binding Sites List in 3git
Zinc binding site 4 out
of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn739
b:57.9
occ:0.75
|
S
|
D:H2S740
|
2.2
|
58.6
|
0.8
|
SG
|
D:CYS595
|
2.2
|
57.5
|
1.0
|
SG
|
D:CYS597
|
2.3
|
57.8
|
1.0
|
SG
|
D:CYS509
|
2.3
|
54.4
|
1.0
|
CB
|
D:CYS509
|
3.2
|
55.7
|
1.0
|
CB
|
D:CYS597
|
3.4
|
57.4
|
1.0
|
CB
|
D:CYS595
|
3.4
|
57.8
|
1.0
|
N
|
D:CYS597
|
3.5
|
57.8
|
1.0
|
FE4
|
D:SF4738
|
3.6
|
56.5
|
1.0
|
S1
|
D:SF4738
|
3.7
|
54.7
|
1.0
|
N
|
D:GLY596
|
3.9
|
58.6
|
1.0
|
CA
|
D:CYS597
|
4.0
|
57.5
|
1.0
|
NH2
|
D:ARG405
|
4.4
|
54.9
|
1.0
|
C
|
D:GLY596
|
4.4
|
58.1
|
1.0
|
CA
|
D:CYS509
|
4.5
|
55.6
|
1.0
|
CD2
|
D:LEU527
|
4.5
|
53.4
|
1.0
|
CA
|
D:CYS595
|
4.6
|
57.9
|
1.0
|
CA
|
D:GLY596
|
4.7
|
57.9
|
1.0
|
C
|
D:CYS595
|
4.7
|
58.6
|
1.0
|
C
|
D:CYS597
|
4.8
|
57.2
|
1.0
|
|
Zinc binding site 5 out
of 6 in 3git
Go back to
Zinc Binding Sites List in 3git
Zinc binding site 5 out
of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn739
b:59.1
occ:0.75
|
S
|
E:H2S740
|
2.2
|
59.8
|
0.8
|
SG
|
E:CYS597
|
2.2
|
57.8
|
1.0
|
SG
|
E:CYS595
|
2.3
|
57.3
|
1.0
|
SG
|
E:CYS509
|
2.4
|
54.9
|
1.0
|
CB
|
E:CYS509
|
3.1
|
55.0
|
1.0
|
CB
|
E:CYS595
|
3.3
|
58.5
|
1.0
|
CB
|
E:CYS597
|
3.4
|
57.2
|
1.0
|
N
|
E:CYS597
|
3.5
|
57.4
|
1.0
|
FE4
|
E:SF4738
|
3.5
|
57.2
|
1.0
|
S1
|
E:SF4738
|
3.8
|
56.0
|
1.0
|
N
|
E:GLY596
|
3.8
|
58.9
|
1.0
|
CA
|
E:CYS597
|
4.0
|
57.3
|
1.0
|
C
|
E:GLY596
|
4.4
|
58.0
|
1.0
|
NH2
|
E:ARG405
|
4.4
|
53.5
|
1.0
|
CA
|
E:CYS509
|
4.4
|
55.2
|
1.0
|
CA
|
E:CYS595
|
4.5
|
58.5
|
1.0
|
CD2
|
E:LEU527
|
4.5
|
53.7
|
1.0
|
CA
|
E:GLY596
|
4.6
|
58.0
|
1.0
|
C
|
E:CYS595
|
4.6
|
58.9
|
1.0
|
C
|
E:CYS597
|
4.9
|
57.3
|
1.0
|
S2
|
E:SF4738
|
5.0
|
57.4
|
1.0
|
|
Zinc binding site 6 out
of 6 in 3git
Go back to
Zinc Binding Sites List in 3git
Zinc binding site 6 out
of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn739
b:57.6
occ:0.75
|
SG
|
F:CYS595
|
2.2
|
57.2
|
1.0
|
SG
|
F:CYS597
|
2.2
|
57.3
|
1.0
|
S
|
F:H2S740
|
2.3
|
59.1
|
0.8
|
SG
|
F:CYS509
|
2.3
|
55.4
|
1.0
|
CB
|
F:CYS509
|
3.1
|
55.2
|
1.0
|
CB
|
F:CYS595
|
3.3
|
57.8
|
1.0
|
N
|
F:CYS597
|
3.5
|
57.9
|
1.0
|
CB
|
F:CYS597
|
3.5
|
58.0
|
1.0
|
FE4
|
F:SF4738
|
3.8
|
56.1
|
1.0
|
N
|
F:GLY596
|
3.8
|
58.2
|
1.0
|
S1
|
F:SF4738
|
3.9
|
55.2
|
1.0
|
CA
|
F:CYS597
|
4.0
|
57.8
|
1.0
|
C
|
F:GLY596
|
4.4
|
58.2
|
1.0
|
NH2
|
F:ARG405
|
4.4
|
53.5
|
1.0
|
CA
|
F:CYS509
|
4.5
|
55.4
|
1.0
|
CD2
|
F:LEU527
|
4.5
|
53.9
|
1.0
|
CA
|
F:CYS595
|
4.5
|
58.0
|
1.0
|
CA
|
F:GLY596
|
4.6
|
58.0
|
1.0
|
C
|
F:CYS595
|
4.6
|
58.4
|
1.0
|
C
|
F:CYS597
|
4.8
|
58.0
|
1.0
|
|
Reference:
A.Volbeda,
C.Darnault,
X.Tan,
P.A.Lindahl,
J.C.Fontecilla-Camps.
Novel Domain Arrangement in the Crystal Structure of A Truncated Acetyl-Coa Synthase From Moorella Thermoacetica Biochemistry V. 48 7916 2009.
ISSN: ISSN 0006-2960
PubMed: 19650626
DOI: 10.1021/BI9003952
Page generated: Thu Oct 24 13:42:56 2024
|