Zinc in PDB 4z3z: Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc
Protein crystallography data
The structure of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc, PDB code: 4z3z
was solved by
T.Weinert,
J.W.Kung,
S.Weidenweber,
S.G.Huwiler,
M.Boll,
U.Ermler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
82.51 /
2.67
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.240,
117.430,
143.080,
90.00,
111.04,
90.00
|
R / Rfree (%)
|
23.2 /
27.4
|
Other elements in 4z3z:
The structure of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc
(pdb code 4z3z). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc, PDB code: 4z3z:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4z3z
Go back to
Zinc Binding Sites List in 4z3z
Zinc binding site 1 out
of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc
![](/pictures/ZN/pdb/z3/4z3z-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/z3/4z3z-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn707
b:67.0
occ:0.18
|
OE1
|
A:GLU257
|
2.0
|
0.3
|
1.0
|
OE2
|
A:GLU257
|
2.0
|
0.9
|
1.0
|
OE1
|
A:GLU251
|
2.0
|
0.0
|
1.0
|
NE2
|
A:HIS255
|
2.1
|
0.9
|
1.0
|
ND1
|
A:HIS260
|
2.1
|
0.3
|
1.0
|
CD
|
A:GLU257
|
2.1
|
0.3
|
1.0
|
OE2
|
A:GLU251
|
2.5
|
0.5
|
1.0
|
CD
|
A:GLU251
|
2.6
|
0.6
|
1.0
|
CE1
|
A:HIS260
|
2.8
|
0.4
|
1.0
|
CE1
|
A:HIS255
|
2.9
|
0.6
|
1.0
|
CD2
|
A:HIS255
|
3.2
|
0.8
|
1.0
|
CG
|
A:HIS260
|
3.2
|
1.0
|
1.0
|
CG
|
A:GLU257
|
3.5
|
0.3
|
1.0
|
CB
|
A:HIS260
|
3.8
|
0.0
|
1.0
|
CD1
|
A:LEU326
|
4.0
|
0.1
|
1.0
|
NE2
|
A:HIS260
|
4.0
|
0.2
|
1.0
|
ND1
|
A:HIS255
|
4.1
|
0.1
|
1.0
|
CG
|
A:GLU251
|
4.1
|
0.1
|
1.0
|
CD2
|
A:HIS260
|
4.2
|
0.6
|
1.0
|
CG
|
A:HIS255
|
4.2
|
0.5
|
1.0
|
CB
|
A:GLU257
|
4.3
|
1.0
|
1.0
|
CA
|
A:GLU257
|
4.3
|
0.4
|
1.0
|
NZ
|
A:LYS325
|
4.6
|
0.5
|
1.0
|
CD1
|
A:ILE242
|
4.7
|
0.9
|
1.0
|
CG
|
A:LEU326
|
4.7
|
0.7
|
1.0
|
CD2
|
A:LEU326
|
4.7
|
0.4
|
1.0
|
CB
|
A:GLU251
|
5.0
|
0.4
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4z3z
Go back to
Zinc Binding Sites List in 4z3z
Zinc binding site 2 out
of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc
![](/pictures/ZN/pdb/z3/4z3z-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/z3/4z3z-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn707
b:40.1
occ:0.26
|
OE2
|
B:GLU257
|
2.0
|
0.2
|
1.0
|
OE1
|
B:GLU257
|
2.0
|
0.6
|
1.0
|
OE1
|
B:GLU251
|
2.0
|
85.4
|
1.0
|
NE2
|
B:HIS255
|
2.1
|
0.3
|
1.0
|
ND1
|
B:HIS260
|
2.1
|
0.7
|
1.0
|
CD
|
B:GLU257
|
2.1
|
0.1
|
1.0
|
OE2
|
B:GLU251
|
2.5
|
79.0
|
1.0
|
CD
|
B:GLU251
|
2.6
|
82.5
|
1.0
|
CE1
|
B:HIS260
|
2.8
|
0.4
|
1.0
|
CE1
|
B:HIS255
|
2.9
|
0.2
|
1.0
|
CD2
|
B:HIS255
|
3.2
|
0.3
|
1.0
|
CG
|
B:HIS260
|
3.2
|
0.7
|
1.0
|
CG
|
B:GLU257
|
3.5
|
0.2
|
1.0
|
CB
|
B:HIS260
|
3.8
|
0.1
|
1.0
|
CD1
|
B:LEU326
|
3.9
|
75.9
|
1.0
|
NE2
|
B:HIS260
|
4.0
|
0.4
|
1.0
|
CG
|
B:GLU251
|
4.1
|
83.1
|
1.0
|
ND1
|
B:HIS255
|
4.1
|
0.6
|
1.0
|
CD2
|
B:HIS260
|
4.2
|
0.3
|
1.0
|
CG
|
B:HIS255
|
4.3
|
0.4
|
1.0
|
CB
|
B:GLU257
|
4.3
|
0.0
|
1.0
|
CA
|
B:GLU257
|
4.3
|
0.3
|
1.0
|
NZ
|
B:LYS325
|
4.5
|
72.4
|
1.0
|
CG
|
B:LEU326
|
4.7
|
75.1
|
1.0
|
CD1
|
B:ILE242
|
4.7
|
0.8
|
1.0
|
CD2
|
B:LEU326
|
4.7
|
74.5
|
1.0
|
CB
|
B:GLU251
|
4.9
|
83.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4z3z
Go back to
Zinc Binding Sites List in 4z3z
Zinc binding site 3 out
of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc
![](/pictures/ZN/pdb/z3/4z3z-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/z3/4z3z-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn707
b:76.6
occ:0.55
|
OE2
|
C:GLU257
|
2.0
|
87.1
|
1.0
|
OE1
|
C:GLU257
|
2.0
|
88.3
|
1.0
|
OE1
|
C:GLU251
|
2.0
|
68.1
|
1.0
|
ND1
|
C:HIS260
|
2.1
|
77.0
|
1.0
|
NE2
|
C:HIS255
|
2.1
|
0.8
|
1.0
|
CD
|
C:GLU257
|
2.1
|
85.7
|
1.0
|
OE2
|
C:GLU251
|
2.5
|
66.9
|
1.0
|
CD
|
C:GLU251
|
2.5
|
67.4
|
1.0
|
CE1
|
C:HIS260
|
2.8
|
77.0
|
1.0
|
CE1
|
C:HIS255
|
2.9
|
0.7
|
1.0
|
CD2
|
C:HIS255
|
3.2
|
0.5
|
1.0
|
CG
|
C:HIS260
|
3.2
|
79.1
|
1.0
|
CG
|
C:GLU257
|
3.5
|
82.6
|
1.0
|
CB
|
C:HIS260
|
3.8
|
79.3
|
1.0
|
CD1
|
C:LEU326
|
3.9
|
59.9
|
1.0
|
NE2
|
C:HIS260
|
4.0
|
78.5
|
1.0
|
CG
|
C:GLU251
|
4.0
|
68.5
|
1.0
|
ND1
|
C:HIS255
|
4.1
|
0.2
|
1.0
|
CD2
|
C:HIS260
|
4.2
|
79.8
|
1.0
|
CG
|
C:HIS255
|
4.3
|
0.6
|
1.0
|
CB
|
C:GLU257
|
4.3
|
81.4
|
1.0
|
CA
|
C:GLU257
|
4.3
|
82.8
|
1.0
|
NZ
|
C:LYS325
|
4.5
|
59.4
|
1.0
|
CG
|
C:LEU326
|
4.6
|
61.0
|
1.0
|
CD2
|
C:LEU326
|
4.7
|
60.1
|
1.0
|
CD1
|
C:ILE242
|
4.7
|
96.7
|
1.0
|
CB
|
C:GLU251
|
4.9
|
65.5
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4z3z
Go back to
Zinc Binding Sites List in 4z3z
Zinc binding site 4 out
of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc
![](/pictures/ZN/pdb/z3/4z3z-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/z3/4z3z-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn707
b:90.0
occ:0.47
|
OE1
|
D:GLU251
|
2.0
|
89.3
|
1.0
|
OE1
|
D:GLU257
|
2.0
|
94.1
|
1.0
|
OE2
|
D:GLU257
|
2.0
|
97.4
|
1.0
|
NE2
|
D:HIS255
|
2.0
|
0.4
|
1.0
|
ND1
|
D:HIS260
|
2.0
|
0.1
|
1.0
|
CD
|
D:GLU257
|
2.2
|
96.1
|
1.0
|
OE2
|
D:GLU251
|
2.6
|
85.5
|
1.0
|
CD
|
D:GLU251
|
2.6
|
86.0
|
1.0
|
CE1
|
D:HIS260
|
2.8
|
0.9
|
1.0
|
CE1
|
D:HIS255
|
2.9
|
0.9
|
1.0
|
CD2
|
D:HIS255
|
3.2
|
0.1
|
1.0
|
CG
|
D:HIS260
|
3.2
|
0.1
|
1.0
|
CG
|
D:GLU257
|
3.5
|
98.2
|
1.0
|
CB
|
D:HIS260
|
3.8
|
0.8
|
1.0
|
NE2
|
D:HIS260
|
4.0
|
0.2
|
1.0
|
CD1
|
D:LEU326
|
4.0
|
83.6
|
1.0
|
ND1
|
D:HIS255
|
4.0
|
0.6
|
1.0
|
CG
|
D:GLU251
|
4.1
|
82.2
|
1.0
|
CD2
|
D:HIS260
|
4.2
|
0.9
|
1.0
|
CG
|
D:HIS255
|
4.2
|
0.4
|
1.0
|
CB
|
D:GLU257
|
4.3
|
99.7
|
1.0
|
CA
|
D:GLU257
|
4.3
|
0.3
|
1.0
|
NZ
|
D:LYS325
|
4.6
|
73.5
|
1.0
|
CD1
|
D:ILE242
|
4.6
|
0.8
|
1.0
|
CG
|
D:LEU326
|
4.7
|
80.0
|
1.0
|
CD2
|
D:LEU326
|
4.8
|
81.6
|
1.0
|
CB
|
D:GLU251
|
5.0
|
80.0
|
1.0
|
N
|
D:GLU257
|
5.0
|
0.5
|
1.0
|
|
Reference:
T.Weinert,
S.G.Huwiler,
J.W.Kung,
S.Weidenweber,
P.Hellwig,
H.J.Stark,
T.Biskup,
S.Weber,
J.J.Cotelesage,
G.N.George,
U.Ermler,
M.Boll.
Structural Basis of Enzymatic Benzene Ring Reduction. Nat.Chem.Biol. V. 11 586 2015.
ISSN: ESSN 1552-4469
PubMed: 26120796
DOI: 10.1038/NCHEMBIO.1849
Page generated: Wed Dec 16 05:58:46 2020
|