Iron in PDB 5xzj: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5
Protein crystallography data
The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5, PDB code: 5xzj
was solved by
W.J.Song,
F.A.Tezcan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
63.89 /
1.98
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.747,
63.481,
127.785,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.7 /
21.7
|
Other elements in 5xzj:
The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5
(pdb code 5xzj). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5, PDB code: 5xzj:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 5xzj
Go back to
Iron Binding Sites List in 5xzj
Iron binding site 1 out
of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:27.2
occ:1.00
|
FE
|
A:HEC201
|
0.0
|
27.2
|
1.0
|
ND
|
A:HEC201
|
1.9
|
27.8
|
1.0
|
NA
|
A:HEC201
|
2.0
|
28.3
|
1.0
|
NB
|
A:HEC201
|
2.1
|
25.6
|
1.0
|
NE2
|
A:HIS102
|
2.1
|
29.7
|
1.0
|
NC
|
A:HEC201
|
2.1
|
26.2
|
1.0
|
SD
|
A:MET7
|
2.3
|
27.8
|
1.0
|
C4D
|
A:HEC201
|
3.0
|
30.8
|
1.0
|
C1D
|
A:HEC201
|
3.0
|
29.7
|
1.0
|
C1A
|
A:HEC201
|
3.0
|
29.5
|
1.0
|
CE1
|
A:HIS102
|
3.1
|
31.3
|
1.0
|
C4B
|
A:HEC201
|
3.1
|
26.2
|
1.0
|
C4A
|
A:HEC201
|
3.1
|
27.8
|
1.0
|
C1B
|
A:HEC201
|
3.1
|
27.0
|
1.0
|
C4C
|
A:HEC201
|
3.1
|
27.3
|
1.0
|
C1C
|
A:HEC201
|
3.1
|
26.3
|
1.0
|
CD2
|
A:HIS102
|
3.1
|
29.2
|
1.0
|
CE
|
A:MET7
|
3.4
|
29.2
|
1.0
|
CHA
|
A:HEC201
|
3.4
|
30.9
|
1.0
|
CG
|
A:MET7
|
3.5
|
26.3
|
1.0
|
CHB
|
A:HEC201
|
3.5
|
28.4
|
1.0
|
CHC
|
A:HEC201
|
3.5
|
25.4
|
1.0
|
CHD
|
A:HEC201
|
3.5
|
26.9
|
1.0
|
ND1
|
A:HIS102
|
4.2
|
29.7
|
1.0
|
CB
|
A:MET7
|
4.2
|
26.8
|
1.0
|
C3D
|
A:HEC201
|
4.3
|
31.8
|
1.0
|
C2D
|
A:HEC201
|
4.3
|
30.0
|
1.0
|
C2A
|
A:HEC201
|
4.3
|
33.8
|
1.0
|
CG
|
A:HIS102
|
4.3
|
28.9
|
1.0
|
C3A
|
A:HEC201
|
4.3
|
29.3
|
1.0
|
C2B
|
A:HEC201
|
4.3
|
26.6
|
1.0
|
C2C
|
A:HEC201
|
4.3
|
25.2
|
1.0
|
C3C
|
A:HEC201
|
4.4
|
25.4
|
1.0
|
C3B
|
A:HEC201
|
4.4
|
24.8
|
1.0
|
NH2
|
A:ARG106
|
4.8
|
68.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 5xzj
Go back to
Iron Binding Sites List in 5xzj
Iron binding site 2 out
of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:25.9
occ:1.00
|
FE
|
B:HEC201
|
0.0
|
25.9
|
1.0
|
ND
|
B:HEC201
|
1.9
|
27.1
|
1.0
|
NA
|
B:HEC201
|
2.0
|
30.0
|
1.0
|
NE2
|
B:HIS102
|
2.0
|
25.9
|
1.0
|
NC
|
B:HEC201
|
2.1
|
26.1
|
1.0
|
NB
|
B:HEC201
|
2.1
|
26.3
|
1.0
|
SD
|
B:MET7
|
2.3
|
26.6
|
1.0
|
C1D
|
B:HEC201
|
3.0
|
26.5
|
1.0
|
C4D
|
B:HEC201
|
3.0
|
28.1
|
1.0
|
CE1
|
B:HIS102
|
3.0
|
26.4
|
1.0
|
C1A
|
B:HEC201
|
3.0
|
29.1
|
1.0
|
C4A
|
B:HEC201
|
3.1
|
29.6
|
1.0
|
CD2
|
B:HIS102
|
3.1
|
29.0
|
1.0
|
C4B
|
B:HEC201
|
3.1
|
26.5
|
1.0
|
C4C
|
B:HEC201
|
3.1
|
25.6
|
1.0
|
C1B
|
B:HEC201
|
3.1
|
27.8
|
1.0
|
C1C
|
B:HEC201
|
3.1
|
26.7
|
1.0
|
CE
|
B:MET7
|
3.4
|
26.9
|
1.0
|
CHA
|
B:HEC201
|
3.4
|
28.8
|
1.0
|
CHD
|
B:HEC201
|
3.4
|
25.0
|
1.0
|
CHB
|
B:HEC201
|
3.5
|
27.7
|
1.0
|
CHC
|
B:HEC201
|
3.5
|
25.0
|
1.0
|
CG
|
B:MET7
|
3.5
|
27.2
|
1.0
|
ND1
|
B:HIS102
|
4.1
|
26.6
|
1.0
|
CG
|
B:HIS102
|
4.2
|
26.6
|
1.0
|
C2D
|
B:HEC201
|
4.2
|
28.3
|
1.0
|
C3A
|
B:HEC201
|
4.2
|
32.7
|
1.0
|
C2A
|
B:HEC201
|
4.3
|
34.8
|
1.0
|
C3D
|
B:HEC201
|
4.3
|
29.5
|
1.0
|
CB
|
B:MET7
|
4.3
|
26.6
|
1.0
|
C2C
|
B:HEC201
|
4.4
|
24.3
|
1.0
|
C3C
|
B:HEC201
|
4.4
|
24.5
|
1.0
|
C2B
|
B:HEC201
|
4.4
|
27.4
|
1.0
|
C3B
|
B:HEC201
|
4.4
|
24.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 5xzj
Go back to
Iron Binding Sites List in 5xzj
Iron binding site 3 out
of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:30.0
occ:1.00
|
FE
|
C:HEC201
|
0.0
|
30.0
|
1.0
|
ND
|
C:HEC201
|
1.9
|
30.8
|
1.0
|
NA
|
C:HEC201
|
2.0
|
33.6
|
1.0
|
NE2
|
C:HIS102
|
2.1
|
30.4
|
1.0
|
NC
|
C:HEC201
|
2.1
|
27.8
|
1.0
|
NB
|
C:HEC201
|
2.1
|
31.1
|
1.0
|
SD
|
C:MET7
|
2.3
|
31.8
|
1.0
|
C4D
|
C:HEC201
|
3.0
|
34.2
|
1.0
|
C1D
|
C:HEC201
|
3.0
|
31.5
|
1.0
|
C1A
|
C:HEC201
|
3.0
|
35.2
|
1.0
|
CE1
|
C:HIS102
|
3.0
|
30.5
|
1.0
|
C4B
|
C:HEC201
|
3.1
|
30.7
|
1.0
|
C4A
|
C:HEC201
|
3.1
|
34.5
|
1.0
|
C1B
|
C:HEC201
|
3.1
|
31.7
|
1.0
|
C1C
|
C:HEC201
|
3.1
|
29.0
|
1.0
|
CD2
|
C:HIS102
|
3.1
|
28.8
|
1.0
|
C4C
|
C:HEC201
|
3.1
|
29.6
|
1.0
|
CHA
|
C:HEC201
|
3.4
|
33.4
|
1.0
|
CHC
|
C:HEC201
|
3.4
|
29.1
|
1.0
|
CHD
|
C:HEC201
|
3.5
|
30.4
|
1.0
|
CE
|
C:MET7
|
3.5
|
31.7
|
1.0
|
CHB
|
C:HEC201
|
3.5
|
32.2
|
1.0
|
CG
|
C:MET7
|
3.5
|
33.7
|
1.0
|
ND1
|
C:HIS102
|
4.2
|
28.4
|
1.0
|
CG
|
C:HIS102
|
4.2
|
28.1
|
1.0
|
C2A
|
C:HEC201
|
4.3
|
38.0
|
1.0
|
C2D
|
C:HEC201
|
4.3
|
32.9
|
1.0
|
C3D
|
C:HEC201
|
4.3
|
34.1
|
1.0
|
C3A
|
C:HEC201
|
4.3
|
36.5
|
1.0
|
CB
|
C:MET7
|
4.3
|
32.4
|
1.0
|
C2B
|
C:HEC201
|
4.3
|
31.7
|
1.0
|
C2C
|
C:HEC201
|
4.3
|
27.9
|
1.0
|
C3B
|
C:HEC201
|
4.4
|
29.6
|
1.0
|
C3C
|
C:HEC201
|
4.4
|
27.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 5xzj
Go back to
Iron Binding Sites List in 5xzj
Iron binding site 4 out
of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:38.3
occ:1.00
|
FE
|
D:HEC201
|
0.0
|
38.3
|
1.0
|
ND
|
D:HEC201
|
1.9
|
37.8
|
1.0
|
NA
|
D:HEC201
|
2.0
|
40.2
|
1.0
|
NB
|
D:HEC201
|
2.1
|
35.8
|
1.0
|
NC
|
D:HEC201
|
2.1
|
37.8
|
1.0
|
NE2
|
D:HIS102
|
2.1
|
28.1
|
1.0
|
SD
|
D:MET7
|
2.4
|
39.4
|
1.0
|
C4D
|
D:HEC201
|
2.9
|
39.5
|
1.0
|
C1D
|
D:HEC201
|
3.0
|
38.5
|
1.0
|
C1A
|
D:HEC201
|
3.0
|
41.8
|
1.0
|
CD2
|
D:HIS102
|
3.0
|
30.6
|
1.0
|
C4B
|
D:HEC201
|
3.1
|
35.6
|
1.0
|
C4A
|
D:HEC201
|
3.1
|
41.5
|
1.0
|
C1B
|
D:HEC201
|
3.1
|
38.0
|
1.0
|
C1C
|
D:HEC201
|
3.1
|
36.0
|
1.0
|
C4C
|
D:HEC201
|
3.1
|
37.9
|
1.0
|
CE1
|
D:HIS102
|
3.1
|
30.3
|
1.0
|
CHA
|
D:HEC201
|
3.4
|
40.0
|
1.0
|
CE
|
D:MET7
|
3.4
|
39.6
|
1.0
|
CHC
|
D:HEC201
|
3.4
|
34.8
|
1.0
|
CHD
|
D:HEC201
|
3.4
|
38.6
|
1.0
|
CHB
|
D:HEC201
|
3.5
|
40.2
|
1.0
|
CG
|
D:MET7
|
3.5
|
41.8
|
1.0
|
C2D
|
D:HEC201
|
4.2
|
38.7
|
1.0
|
CG
|
D:HIS102
|
4.2
|
31.8
|
1.0
|
C3D
|
D:HEC201
|
4.2
|
40.1
|
1.0
|
ND1
|
D:HIS102
|
4.2
|
29.8
|
1.0
|
C2A
|
D:HEC201
|
4.2
|
46.3
|
1.0
|
C3A
|
D:HEC201
|
4.3
|
44.8
|
1.0
|
C2C
|
D:HEC201
|
4.3
|
37.7
|
1.0
|
CB
|
D:MET7
|
4.3
|
38.3
|
1.0
|
C2B
|
D:HEC201
|
4.3
|
35.6
|
1.0
|
C3C
|
D:HEC201
|
4.3
|
37.6
|
1.0
|
C3B
|
D:HEC201
|
4.3
|
34.4
|
1.0
|
|
Reference:
W.J.Song,
J.Yu,
F.A.Tezcan.
Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-Beta-Lactamases. J. Am. Chem. Soc. V. 139 16772 2017.
ISSN: ESSN 1520-5126
PubMed: 28992705
DOI: 10.1021/JACS.7B08981
Page generated: Tue Aug 6 12:36:34 2024
|