Iron in PDB 6ai5: Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3
Protein crystallography data
The structure of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3, PDB code: 6ai5
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)
|
36.60 /
1.81
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.562,
76.871,
96.425,
90.00,
105.84,
90.00
|
R / Rfree (%)
|
17.5 /
20.9
|
Other elements in 6ai5:
The structure of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3
(pdb code 6ai5). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3, PDB code: 6ai5:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6ai5
Go back to
Iron Binding Sites List in 6ai5
Iron binding site 1 out
of 4 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:20.1
occ:1.00
|
FE
|
A:HEM201
|
0.0
|
20.1
|
1.0
|
ND
|
A:HEM201
|
1.9
|
20.9
|
1.0
|
NE2
|
A:HIS102
|
2.0
|
20.4
|
1.0
|
NA
|
A:HEM201
|
2.0
|
21.5
|
1.0
|
NC
|
A:HEM201
|
2.1
|
18.6
|
1.0
|
NB
|
A:HEM201
|
2.1
|
19.8
|
1.0
|
SD
|
A:MET7
|
2.3
|
18.6
|
1.0
|
C4D
|
A:HEM201
|
2.9
|
20.2
|
1.0
|
C1D
|
A:HEM201
|
3.0
|
18.8
|
1.0
|
CE1
|
A:HIS102
|
3.0
|
20.4
|
1.0
|
C1A
|
A:HEM201
|
3.0
|
22.4
|
1.0
|
CD2
|
A:HIS102
|
3.0
|
20.1
|
1.0
|
C4C
|
A:HEM201
|
3.0
|
18.2
|
1.0
|
C4B
|
A:HEM201
|
3.0
|
17.9
|
1.0
|
C4A
|
A:HEM201
|
3.1
|
21.3
|
1.0
|
C1B
|
A:HEM201
|
3.1
|
19.7
|
1.0
|
C1C
|
A:HEM201
|
3.1
|
17.2
|
1.0
|
CE
|
A:MET7
|
3.3
|
19.4
|
1.0
|
CHA
|
A:HEM201
|
3.4
|
21.9
|
1.0
|
CHD
|
A:HEM201
|
3.4
|
19.3
|
1.0
|
CG
|
A:MET7
|
3.4
|
18.1
|
1.0
|
CHC
|
A:HEM201
|
3.5
|
16.9
|
1.0
|
CHB
|
A:HEM201
|
3.5
|
20.7
|
1.0
|
ND1
|
A:HIS102
|
4.1
|
20.1
|
1.0
|
CG
|
A:HIS102
|
4.1
|
19.4
|
1.0
|
CB
|
A:MET7
|
4.2
|
18.8
|
1.0
|
C2A
|
A:HEM201
|
4.2
|
24.6
|
1.0
|
C3D
|
A:HEM201
|
4.2
|
21.9
|
1.0
|
C2D
|
A:HEM201
|
4.2
|
20.7
|
1.0
|
C3A
|
A:HEM201
|
4.2
|
23.7
|
1.0
|
C3C
|
A:HEM201
|
4.3
|
17.7
|
1.0
|
C2C
|
A:HEM201
|
4.3
|
16.8
|
1.0
|
C2B
|
A:HEM201
|
4.3
|
18.4
|
1.0
|
C3B
|
A:HEM201
|
4.3
|
17.9
|
1.0
|
CA
|
A:MET7
|
5.0
|
18.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 6ai5
Go back to
Iron Binding Sites List in 6ai5
Iron binding site 2 out
of 4 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:17.5
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
17.5
|
1.0
|
ND
|
C:HEM201
|
1.9
|
18.4
|
1.0
|
NA
|
C:HEM201
|
2.0
|
18.4
|
1.0
|
NE2
|
C:HIS102
|
2.0
|
17.5
|
1.0
|
NB
|
C:HEM201
|
2.1
|
17.4
|
1.0
|
NC
|
C:HEM201
|
2.1
|
17.2
|
1.0
|
SD
|
C:MET7
|
2.3
|
18.0
|
1.0
|
C4D
|
C:HEM201
|
2.9
|
18.2
|
1.0
|
CE1
|
C:HIS102
|
3.0
|
17.6
|
1.0
|
C1D
|
C:HEM201
|
3.0
|
16.8
|
1.0
|
C1A
|
C:HEM201
|
3.0
|
19.1
|
1.0
|
C4A
|
C:HEM201
|
3.0
|
18.4
|
1.0
|
C4B
|
C:HEM201
|
3.0
|
16.7
|
1.0
|
C1B
|
C:HEM201
|
3.1
|
17.8
|
1.0
|
CD2
|
C:HIS102
|
3.1
|
17.6
|
1.0
|
C4C
|
C:HEM201
|
3.1
|
16.5
|
1.0
|
C1C
|
C:HEM201
|
3.1
|
16.4
|
1.0
|
CE
|
C:MET7
|
3.3
|
19.6
|
1.0
|
CHA
|
C:HEM201
|
3.3
|
19.4
|
1.0
|
CG
|
C:MET7
|
3.4
|
18.1
|
1.0
|
CHB
|
C:HEM201
|
3.4
|
16.9
|
1.0
|
CHD
|
C:HEM201
|
3.5
|
16.6
|
1.0
|
CHC
|
C:HEM201
|
3.5
|
16.8
|
1.0
|
CB
|
C:MET7
|
4.1
|
17.6
|
1.0
|
ND1
|
C:HIS102
|
4.1
|
18.2
|
1.0
|
CG
|
C:HIS102
|
4.2
|
17.9
|
1.0
|
C2A
|
C:HEM201
|
4.2
|
19.9
|
1.0
|
C3A
|
C:HEM201
|
4.2
|
19.3
|
1.0
|
C3D
|
C:HEM201
|
4.2
|
20.8
|
1.0
|
C2D
|
C:HEM201
|
4.2
|
18.9
|
1.0
|
C2B
|
C:HEM201
|
4.3
|
17.2
|
1.0
|
C2C
|
C:HEM201
|
4.3
|
16.2
|
1.0
|
C3C
|
C:HEM201
|
4.3
|
15.7
|
1.0
|
C3B
|
C:HEM201
|
4.3
|
16.6
|
1.0
|
CA
|
C:MET7
|
4.9
|
17.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 6ai5
Go back to
Iron Binding Sites List in 6ai5
Iron binding site 3 out
of 4 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:19.1
occ:1.00
|
FE
|
E:HEM201
|
0.0
|
19.1
|
1.0
|
ND
|
E:HEM201
|
1.9
|
20.8
|
1.0
|
NE2
|
E:HIS102
|
2.0
|
19.3
|
1.0
|
NA
|
E:HEM201
|
2.0
|
22.4
|
1.0
|
NB
|
E:HEM201
|
2.1
|
19.9
|
1.0
|
NC
|
E:HEM201
|
2.1
|
18.8
|
1.0
|
SD
|
E:MET7
|
2.3
|
20.1
|
1.0
|
C4D
|
E:HEM201
|
2.9
|
23.2
|
1.0
|
C1D
|
E:HEM201
|
2.9
|
21.2
|
1.0
|
CE1
|
E:HIS102
|
3.0
|
19.1
|
1.0
|
C1A
|
E:HEM201
|
3.0
|
24.2
|
1.0
|
CD2
|
E:HIS102
|
3.0
|
19.4
|
1.0
|
C4B
|
E:HEM201
|
3.0
|
18.8
|
1.0
|
C4A
|
E:HEM201
|
3.1
|
23.1
|
1.0
|
C1B
|
E:HEM201
|
3.1
|
19.6
|
1.0
|
C1C
|
E:HEM201
|
3.1
|
18.9
|
1.0
|
C4C
|
E:HEM201
|
3.1
|
18.9
|
1.0
|
CHA
|
E:HEM201
|
3.4
|
22.9
|
1.0
|
CE
|
E:MET7
|
3.4
|
21.5
|
1.0
|
CG
|
E:MET7
|
3.4
|
19.6
|
1.0
|
CHC
|
E:HEM201
|
3.4
|
18.6
|
1.0
|
CHD
|
E:HEM201
|
3.4
|
19.7
|
1.0
|
CHB
|
E:HEM201
|
3.5
|
21.7
|
1.0
|
ND1
|
E:HIS102
|
4.1
|
19.1
|
1.0
|
CG
|
E:HIS102
|
4.1
|
19.0
|
1.0
|
CB
|
E:MET7
|
4.2
|
19.6
|
1.0
|
C2D
|
E:HEM201
|
4.2
|
22.6
|
1.0
|
C3D
|
E:HEM201
|
4.2
|
24.6
|
1.0
|
C2A
|
E:HEM201
|
4.2
|
27.8
|
1.0
|
C3A
|
E:HEM201
|
4.2
|
25.9
|
1.0
|
C2B
|
E:HEM201
|
4.3
|
19.2
|
1.0
|
C2C
|
E:HEM201
|
4.3
|
18.4
|
1.0
|
C3B
|
E:HEM201
|
4.3
|
18.9
|
1.0
|
C3C
|
E:HEM201
|
4.3
|
17.4
|
1.0
|
NH2
|
E:ARG106
|
4.9
|
43.3
|
1.0
|
CA
|
E:MET7
|
5.0
|
20.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 6ai5
Go back to
Iron Binding Sites List in 6ai5
Iron binding site 4 out
of 4 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe201
b:21.2
occ:1.00
|
FE
|
G:HEM201
|
0.0
|
21.2
|
1.0
|
ND
|
G:HEM201
|
1.9
|
22.7
|
1.0
|
NE2
|
G:HIS102
|
2.0
|
19.4
|
1.0
|
NA
|
G:HEM201
|
2.0
|
22.5
|
1.0
|
NC
|
G:HEM201
|
2.1
|
20.0
|
1.0
|
NB
|
G:HEM201
|
2.1
|
21.7
|
1.0
|
SD
|
G:MET7
|
2.3
|
20.8
|
1.0
|
C4D
|
G:HEM201
|
2.9
|
23.8
|
1.0
|
C1D
|
G:HEM201
|
2.9
|
22.6
|
1.0
|
CE1
|
G:HIS102
|
3.0
|
20.6
|
1.0
|
C1A
|
G:HEM201
|
3.0
|
24.1
|
1.0
|
CD2
|
G:HIS102
|
3.0
|
20.8
|
1.0
|
C4A
|
G:HEM201
|
3.0
|
22.6
|
1.0
|
C4B
|
G:HEM201
|
3.1
|
20.7
|
1.0
|
C4C
|
G:HEM201
|
3.1
|
20.2
|
1.0
|
C1B
|
G:HEM201
|
3.1
|
22.2
|
1.0
|
C1C
|
G:HEM201
|
3.1
|
19.5
|
1.0
|
CHA
|
G:HEM201
|
3.4
|
24.1
|
1.0
|
CE
|
G:MET7
|
3.4
|
19.8
|
1.0
|
CHD
|
G:HEM201
|
3.4
|
21.4
|
1.0
|
CHC
|
G:HEM201
|
3.4
|
19.4
|
1.0
|
CG
|
G:MET7
|
3.5
|
19.4
|
1.0
|
CHB
|
G:HEM201
|
3.5
|
21.6
|
1.0
|
ND1
|
G:HIS102
|
4.1
|
19.4
|
1.0
|
CG
|
G:HIS102
|
4.2
|
20.9
|
1.0
|
CB
|
G:MET7
|
4.2
|
19.6
|
1.0
|
C3D
|
G:HEM201
|
4.2
|
26.2
|
1.0
|
C2A
|
G:HEM201
|
4.2
|
25.3
|
1.0
|
C2D
|
G:HEM201
|
4.2
|
24.3
|
1.0
|
C3A
|
G:HEM201
|
4.2
|
24.1
|
1.0
|
C2C
|
G:HEM201
|
4.3
|
19.2
|
1.0
|
C3C
|
G:HEM201
|
4.3
|
20.1
|
1.0
|
C2B
|
G:HEM201
|
4.3
|
20.9
|
1.0
|
C3B
|
G:HEM201
|
4.3
|
20.6
|
1.0
|
CA
|
G:MET7
|
5.0
|
19.6
|
1.0
|
|
Reference:
W.J.Song,
F.A.Tezcan.
Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 To Be Published.
Page generated: Tue Aug 6 13:35:14 2024
|