Iron in PDB 1u9m: Crystal Structure of F58W Mutant of Cytochrome B5
Protein crystallography data
The structure of Crystal Structure of F58W Mutant of Cytochrome B5, PDB code: 1u9m
was solved by
L.Shan,
J.-X.Lu,
J.-H.Gan,
Y.-H.Wang,
Z.-X.Huang,
Z.-X.Xia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
35.55 /
2.00
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.044,
87.484,
138.383,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
22.4 /
26.6
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of F58W Mutant of Cytochrome B5
(pdb code 1u9m). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of F58W Mutant of Cytochrome B5, PDB code: 1u9m:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1u9m
Go back to
Iron Binding Sites List in 1u9m
Iron binding site 1 out
of 6 in the Crystal Structure of F58W Mutant of Cytochrome B5
 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 F58W Mutant of Cytochrome B5 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe90
b:22.9
occ:1.00
|
FE
|
A:HEM90
|
0.0
|
22.9
|
1.0
|
|
NB
|
A:HEM90
|
2.0
|
23.3
|
1.0
|
|
ND
|
A:HEM90
|
2.0
|
24.3
|
1.0
|
|
NC
|
A:HEM90
|
2.0
|
20.8
|
1.0
|
|
NA
|
A:HEM90
|
2.0
|
23.9
|
1.0
|
|
NE2
|
A:HIS63
|
2.1
|
23.2
|
1.0
|
|
NE2
|
A:HIS39
|
2.1
|
25.6
|
1.0
|
|
CE1
|
A:HIS39
|
3.0
|
26.2
|
1.0
|
|
C4B
|
A:HEM90
|
3.0
|
23.1
|
1.0
|
|
C1C
|
A:HEM90
|
3.0
|
21.5
|
1.0
|
|
C1A
|
A:HEM90
|
3.0
|
24.7
|
1.0
|
|
C4D
|
A:HEM90
|
3.0
|
25.6
|
1.0
|
|
C1B
|
A:HEM90
|
3.0
|
23.6
|
1.0
|
|
C1D
|
A:HEM90
|
3.0
|
24.4
|
1.0
|
|
C4C
|
A:HEM90
|
3.1
|
23.5
|
1.0
|
|
CD2
|
A:HIS63
|
3.1
|
24.1
|
1.0
|
|
C4A
|
A:HEM90
|
3.1
|
24.6
|
1.0
|
|
CE1
|
A:HIS63
|
3.1
|
23.3
|
1.0
|
|
CD2
|
A:HIS39
|
3.2
|
24.8
|
1.0
|
|
CHC
|
A:HEM90
|
3.4
|
20.7
|
1.0
|
|
CHA
|
A:HEM90
|
3.4
|
24.6
|
1.0
|
|
CHB
|
A:HEM90
|
3.4
|
25.1
|
1.0
|
|
CHD
|
A:HEM90
|
3.5
|
22.9
|
1.0
|
|
ND1
|
A:HIS39
|
4.2
|
28.0
|
1.0
|
|
CG
|
A:HIS63
|
4.2
|
25.4
|
1.0
|
|
C3B
|
A:HEM90
|
4.2
|
25.6
|
1.0
|
|
ND1
|
A:HIS63
|
4.2
|
23.7
|
1.0
|
|
C2B
|
A:HEM90
|
4.3
|
23.7
|
1.0
|
|
C3D
|
A:HEM90
|
4.3
|
26.5
|
1.0
|
|
C2A
|
A:HEM90
|
4.3
|
26.9
|
1.0
|
|
C2D
|
A:HEM90
|
4.3
|
26.2
|
1.0
|
|
C2C
|
A:HEM90
|
4.3
|
22.7
|
1.0
|
|
C3C
|
A:HEM90
|
4.3
|
23.5
|
1.0
|
|
C3A
|
A:HEM90
|
4.3
|
26.3
|
1.0
|
|
CG
|
A:HIS39
|
4.3
|
27.4
|
1.0
|
|
CZ3
|
A:TRP58
|
4.8
|
30.5
|
1.0
|
|
Iron binding site 2 out
of 6 in 1u9m
Go back to
Iron Binding Sites List in 1u9m
Iron binding site 2 out
of 6 in the Crystal Structure of F58W Mutant of Cytochrome B5
 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 F58W Mutant of Cytochrome B5 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe90
b:19.8
occ:1.00
|
FE
|
B:HEM90
|
0.0
|
19.8
|
1.0
|
|
ND
|
B:HEM90
|
1.9
|
19.2
|
1.0
|
|
NB
|
B:HEM90
|
2.0
|
21.7
|
1.0
|
|
NA
|
B:HEM90
|
2.0
|
19.1
|
1.0
|
|
NC
|
B:HEM90
|
2.0
|
18.9
|
1.0
|
|
NE2
|
B:HIS39
|
2.0
|
21.1
|
1.0
|
|
NE2
|
B:HIS63
|
2.1
|
20.6
|
1.0
|
|
C4D
|
B:HEM90
|
3.0
|
19.7
|
1.0
|
|
C1A
|
B:HEM90
|
3.0
|
20.0
|
1.0
|
|
C4B
|
B:HEM90
|
3.0
|
21.8
|
1.0
|
|
C1D
|
B:HEM90
|
3.0
|
19.4
|
1.0
|
|
C1C
|
B:HEM90
|
3.0
|
18.6
|
1.0
|
|
CE1
|
B:HIS39
|
3.0
|
23.7
|
1.0
|
|
C4A
|
B:HEM90
|
3.0
|
19.7
|
1.0
|
|
C1B
|
B:HEM90
|
3.1
|
20.9
|
1.0
|
|
CD2
|
B:HIS39
|
3.1
|
20.9
|
1.0
|
|
C4C
|
B:HEM90
|
3.1
|
17.7
|
1.0
|
|
CE1
|
B:HIS63
|
3.1
|
20.4
|
1.0
|
|
CD2
|
B:HIS63
|
3.1
|
20.4
|
1.0
|
|
CHA
|
B:HEM90
|
3.4
|
18.7
|
1.0
|
|
CHC
|
B:HEM90
|
3.4
|
20.0
|
1.0
|
|
CHD
|
B:HEM90
|
3.4
|
16.0
|
1.0
|
|
CHB
|
B:HEM90
|
3.4
|
20.6
|
1.0
|
|
ND1
|
B:HIS39
|
4.2
|
22.8
|
1.0
|
|
CG
|
B:HIS39
|
4.2
|
24.6
|
1.0
|
|
C3D
|
B:HEM90
|
4.2
|
22.4
|
1.0
|
|
ND1
|
B:HIS63
|
4.2
|
21.9
|
1.0
|
|
C2D
|
B:HEM90
|
4.2
|
21.2
|
1.0
|
|
CG
|
B:HIS63
|
4.2
|
20.9
|
1.0
|
|
C3B
|
B:HEM90
|
4.3
|
22.7
|
1.0
|
|
C2A
|
B:HEM90
|
4.3
|
21.1
|
1.0
|
|
C2B
|
B:HEM90
|
4.3
|
21.2
|
1.0
|
|
C3A
|
B:HEM90
|
4.3
|
20.6
|
1.0
|
|
C2C
|
B:HEM90
|
4.3
|
17.9
|
1.0
|
|
C3C
|
B:HEM90
|
4.3
|
17.5
|
1.0
|
|
CZ3
|
B:TRP58
|
4.8
|
29.6
|
1.0
|
|
CE3
|
B:TRP58
|
5.0
|
27.6
|
1.0
|
|
N
|
B:GLY41
|
5.0
|
28.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 1u9m
Go back to
Iron Binding Sites List in 1u9m
Iron binding site 3 out
of 6 in the Crystal Structure of F58W Mutant of Cytochrome B5
 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 F58W Mutant of Cytochrome B5 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe90
b:21.0
occ:1.00
|
FE
|
C:HEM90
|
0.0
|
21.0
|
1.0
|
|
ND
|
C:HEM90
|
2.0
|
20.2
|
1.0
|
|
NC
|
C:HEM90
|
2.0
|
17.7
|
1.0
|
|
NB
|
C:HEM90
|
2.0
|
21.7
|
1.0
|
|
NA
|
C:HEM90
|
2.0
|
19.8
|
1.0
|
|
NE2
|
C:HIS63
|
2.1
|
20.2
|
1.0
|
|
NE2
|
C:HIS39
|
2.1
|
19.8
|
1.0
|
|
C1C
|
C:HEM90
|
3.0
|
18.6
|
1.0
|
|
C4D
|
C:HEM90
|
3.0
|
19.2
|
1.0
|
|
C4B
|
C:HEM90
|
3.0
|
19.9
|
1.0
|
|
C1D
|
C:HEM90
|
3.0
|
17.0
|
1.0
|
|
C1A
|
C:HEM90
|
3.0
|
19.7
|
1.0
|
|
C4C
|
C:HEM90
|
3.1
|
16.9
|
1.0
|
|
C1B
|
C:HEM90
|
3.1
|
21.4
|
1.0
|
|
C4A
|
C:HEM90
|
3.1
|
22.2
|
1.0
|
|
CE1
|
C:HIS39
|
3.1
|
23.2
|
1.0
|
|
CD2
|
C:HIS63
|
3.1
|
21.6
|
1.0
|
|
CE1
|
C:HIS63
|
3.1
|
21.4
|
1.0
|
|
CD2
|
C:HIS39
|
3.1
|
22.6
|
1.0
|
|
CHC
|
C:HEM90
|
3.4
|
19.6
|
1.0
|
|
CHA
|
C:HEM90
|
3.4
|
19.2
|
1.0
|
|
CHD
|
C:HEM90
|
3.4
|
17.3
|
1.0
|
|
CHB
|
C:HEM90
|
3.5
|
19.8
|
1.0
|
|
ND1
|
C:HIS39
|
4.2
|
21.2
|
1.0
|
|
ND1
|
C:HIS63
|
4.2
|
17.5
|
1.0
|
|
CG
|
C:HIS63
|
4.2
|
22.2
|
1.0
|
|
C3D
|
C:HEM90
|
4.3
|
21.5
|
1.0
|
|
C2D
|
C:HEM90
|
4.3
|
21.1
|
1.0
|
|
C2C
|
C:HEM90
|
4.3
|
19.6
|
1.0
|
|
CG
|
C:HIS39
|
4.3
|
22.9
|
1.0
|
|
C2B
|
C:HEM90
|
4.3
|
24.4
|
1.0
|
|
C2A
|
C:HEM90
|
4.3
|
21.9
|
1.0
|
|
C3B
|
C:HEM90
|
4.3
|
24.8
|
1.0
|
|
C3A
|
C:HEM90
|
4.3
|
20.7
|
1.0
|
|
C3C
|
C:HEM90
|
4.3
|
20.9
|
1.0
|
|
CZ3
|
C:TRP58
|
4.9
|
19.2
|
1.0
|
|
Iron binding site 4 out
of 6 in 1u9m
Go back to
Iron Binding Sites List in 1u9m
Iron binding site 4 out
of 6 in the Crystal Structure of F58W Mutant of Cytochrome B5
 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 F58W Mutant of Cytochrome B5 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe90
b:27.3
occ:1.00
|
FE
|
D:HEM90
|
0.0
|
27.3
|
1.0
|
|
NA
|
D:HEM90
|
2.0
|
27.9
|
1.0
|
|
ND
|
D:HEM90
|
2.0
|
27.5
|
1.0
|
|
NB
|
D:HEM90
|
2.0
|
26.7
|
1.0
|
|
NC
|
D:HEM90
|
2.0
|
22.6
|
1.0
|
|
NE2
|
D:HIS63
|
2.0
|
27.8
|
1.0
|
|
NE2
|
D:HIS39
|
2.1
|
28.8
|
1.0
|
|
CD2
|
D:HIS63
|
3.0
|
26.8
|
1.0
|
|
C1A
|
D:HEM90
|
3.0
|
28.0
|
1.0
|
|
C4A
|
D:HEM90
|
3.0
|
28.5
|
1.0
|
|
C4D
|
D:HEM90
|
3.0
|
29.1
|
1.0
|
|
C1C
|
D:HEM90
|
3.0
|
23.9
|
1.0
|
|
CE1
|
D:HIS39
|
3.0
|
30.7
|
1.0
|
|
C1D
|
D:HEM90
|
3.1
|
26.4
|
1.0
|
|
C1B
|
D:HEM90
|
3.1
|
27.5
|
1.0
|
|
C4B
|
D:HEM90
|
3.1
|
27.0
|
1.0
|
|
C4C
|
D:HEM90
|
3.1
|
23.4
|
1.0
|
|
CE1
|
D:HIS63
|
3.1
|
27.1
|
1.0
|
|
CD2
|
D:HIS39
|
3.2
|
30.8
|
1.0
|
|
CHA
|
D:HEM90
|
3.4
|
29.4
|
1.0
|
|
CHC
|
D:HEM90
|
3.4
|
24.1
|
1.0
|
|
CHB
|
D:HEM90
|
3.4
|
28.9
|
1.0
|
|
CHD
|
D:HEM90
|
3.5
|
24.6
|
1.0
|
|
CG
|
D:HIS63
|
4.2
|
29.6
|
1.0
|
|
ND1
|
D:HIS63
|
4.2
|
30.3
|
1.0
|
|
ND1
|
D:HIS39
|
4.2
|
34.7
|
1.0
|
|
C2A
|
D:HEM90
|
4.3
|
30.5
|
1.0
|
|
C3A
|
D:HEM90
|
4.3
|
31.0
|
1.0
|
|
C2D
|
D:HEM90
|
4.3
|
28.2
|
1.0
|
|
C3D
|
D:HEM90
|
4.3
|
30.4
|
1.0
|
|
C2B
|
D:HEM90
|
4.3
|
27.7
|
1.0
|
|
C2C
|
D:HEM90
|
4.3
|
22.2
|
1.0
|
|
CG
|
D:HIS39
|
4.3
|
34.0
|
1.0
|
|
C3C
|
D:HEM90
|
4.3
|
25.1
|
1.0
|
|
C3B
|
D:HEM90
|
4.3
|
28.0
|
1.0
|
|
CZ3
|
D:TRP58
|
4.7
|
33.6
|
1.0
|
|
CE3
|
D:TRP58
|
4.9
|
32.0
|
1.0
|
|
N
|
D:GLY41
|
5.0
|
36.6
|
1.0
|
|
Iron binding site 5 out
of 6 in 1u9m
Go back to
Iron Binding Sites List in 1u9m
Iron binding site 5 out
of 6 in the Crystal Structure of F58W Mutant of Cytochrome B5
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of F58W Mutant of Cytochrome B5 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe90
b:22.1
occ:1.00
|
FE
|
E:HEM90
|
0.0
|
22.1
|
1.0
|
|
NC
|
E:HEM90
|
2.0
|
20.6
|
1.0
|
|
NA
|
E:HEM90
|
2.0
|
22.8
|
1.0
|
|
ND
|
E:HEM90
|
2.0
|
22.4
|
1.0
|
|
NB
|
E:HEM90
|
2.0
|
24.1
|
1.0
|
|
NE2
|
E:HIS63
|
2.0
|
20.7
|
1.0
|
|
NE2
|
E:HIS39
|
2.1
|
22.3
|
1.0
|
|
C1C
|
E:HEM90
|
3.0
|
22.5
|
1.0
|
|
CD2
|
E:HIS63
|
3.0
|
23.1
|
1.0
|
|
C1A
|
E:HEM90
|
3.0
|
24.0
|
1.0
|
|
C4C
|
E:HEM90
|
3.0
|
20.9
|
1.0
|
|
C4B
|
E:HEM90
|
3.0
|
24.8
|
1.0
|
|
C4D
|
E:HEM90
|
3.0
|
23.0
|
1.0
|
|
C1D
|
E:HEM90
|
3.0
|
20.4
|
1.0
|
|
C4A
|
E:HEM90
|
3.1
|
25.8
|
1.0
|
|
C1B
|
E:HEM90
|
3.1
|
25.4
|
1.0
|
|
CE1
|
E:HIS63
|
3.1
|
20.4
|
1.0
|
|
CD2
|
E:HIS39
|
3.1
|
23.0
|
1.0
|
|
CE1
|
E:HIS39
|
3.1
|
23.9
|
1.0
|
|
CHC
|
E:HEM90
|
3.4
|
21.6
|
1.0
|
|
CHA
|
E:HEM90
|
3.4
|
25.0
|
1.0
|
|
CHD
|
E:HEM90
|
3.4
|
20.3
|
1.0
|
|
CHB
|
E:HEM90
|
3.5
|
25.0
|
1.0
|
|
CG
|
E:HIS63
|
4.2
|
23.6
|
1.0
|
|
ND1
|
E:HIS63
|
4.2
|
19.5
|
1.0
|
|
C2C
|
E:HEM90
|
4.2
|
21.3
|
1.0
|
|
C2A
|
E:HEM90
|
4.3
|
26.7
|
1.0
|
|
C2D
|
E:HEM90
|
4.3
|
23.5
|
1.0
|
|
ND1
|
E:HIS39
|
4.3
|
24.6
|
1.0
|
|
CG
|
E:HIS39
|
4.3
|
27.0
|
1.0
|
|
C3C
|
E:HEM90
|
4.3
|
23.1
|
1.0
|
|
C3B
|
E:HEM90
|
4.3
|
27.2
|
1.0
|
|
C2B
|
E:HEM90
|
4.3
|
27.2
|
1.0
|
|
C3A
|
E:HEM90
|
4.3
|
24.2
|
1.0
|
|
C3D
|
E:HEM90
|
4.3
|
25.2
|
1.0
|
|
CZ3
|
E:TRP58
|
4.9
|
22.7
|
1.0
|
|
Iron binding site 6 out
of 6 in 1u9m
Go back to
Iron Binding Sites List in 1u9m
Iron binding site 6 out
of 6 in the Crystal Structure of F58W Mutant of Cytochrome B5
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of F58W Mutant of Cytochrome B5 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe90
b:22.4
occ:1.00
|
FE
|
F:HEM90
|
0.0
|
22.4
|
1.0
|
|
NB
|
F:HEM90
|
2.0
|
22.9
|
1.0
|
|
ND
|
F:HEM90
|
2.0
|
21.1
|
1.0
|
|
NC
|
F:HEM90
|
2.0
|
23.0
|
1.0
|
|
NA
|
F:HEM90
|
2.0
|
23.0
|
1.0
|
|
NE2
|
F:HIS63
|
2.1
|
22.7
|
1.0
|
|
NE2
|
F:HIS39
|
2.1
|
24.4
|
1.0
|
|
C1C
|
F:HEM90
|
3.0
|
21.7
|
1.0
|
|
C4B
|
F:HEM90
|
3.0
|
24.2
|
1.0
|
|
CD2
|
F:HIS63
|
3.0
|
24.0
|
1.0
|
|
C1A
|
F:HEM90
|
3.0
|
22.6
|
1.0
|
|
C4D
|
F:HEM90
|
3.0
|
20.6
|
1.0
|
|
C1B
|
F:HEM90
|
3.1
|
23.7
|
1.0
|
|
C4A
|
F:HEM90
|
3.1
|
23.5
|
1.0
|
|
C1D
|
F:HEM90
|
3.1
|
20.8
|
1.0
|
|
C4C
|
F:HEM90
|
3.1
|
22.2
|
1.0
|
|
CE1
|
F:HIS63
|
3.1
|
22.3
|
1.0
|
|
CE1
|
F:HIS39
|
3.1
|
26.3
|
1.0
|
|
CD2
|
F:HIS39
|
3.1
|
26.4
|
1.0
|
|
CHC
|
F:HEM90
|
3.4
|
20.3
|
1.0
|
|
CHA
|
F:HEM90
|
3.4
|
19.3
|
1.0
|
|
CHB
|
F:HEM90
|
3.5
|
23.3
|
1.0
|
|
CHD
|
F:HEM90
|
3.5
|
20.3
|
1.0
|
|
ND1
|
F:HIS63
|
4.2
|
22.1
|
1.0
|
|
CG
|
F:HIS63
|
4.2
|
23.5
|
1.0
|
|
C3B
|
F:HEM90
|
4.2
|
26.2
|
1.0
|
|
C2C
|
F:HEM90
|
4.2
|
23.5
|
1.0
|
|
ND1
|
F:HIS39
|
4.3
|
27.0
|
1.0
|
|
C2B
|
F:HEM90
|
4.3
|
25.3
|
1.0
|
|
C2D
|
F:HEM90
|
4.3
|
21.6
|
1.0
|
|
C3A
|
F:HEM90
|
4.3
|
24.7
|
1.0
|
|
C2A
|
F:HEM90
|
4.3
|
23.8
|
1.0
|
|
C3D
|
F:HEM90
|
4.3
|
21.9
|
1.0
|
|
CG
|
F:HIS39
|
4.3
|
29.9
|
1.0
|
|
C3C
|
F:HEM90
|
4.3
|
22.9
|
1.0
|
|
CZ3
|
F:TRP58
|
4.8
|
24.1
|
1.0
|
|
CE3
|
F:TRP58
|
5.0
|
21.9
|
1.0
|
|
Reference:
L.Shan,
J.X.Lu,
J.H.Gan,
Y.H.Wang,
Z.X.Huang,
Z.X.Xia.
Structure of the F58W Mutant of Cytochrome B5: the Mutation Leads to Multiple Conformations and Weakens Stacking Interactions. Acta Crystallogr.,Sect.D V. 61 180 2005.
ISSN: ISSN 0907-4449
PubMed: 15681869
DOI: 10.1107/S0907444904031798
Page generated: Sat Aug 3 15:25:40 2024
|
