Iron in PDB 4h0j: Mutant M58C of Nostoc Sp Cytochrome C6
Protein crystallography data
The structure of Mutant M58C of Nostoc Sp Cytochrome C6, PDB code: 4h0j
was solved by
N.S.Pannu,
P.Skubak,
M.Ubbink,
D.Cavazzini,
G.L.Rossi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
26.72 /
2.00
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.823,
80.157,
80.147,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
20.7 /
24.6
|
Iron Binding Sites:
The binding sites of Iron atom in the Mutant M58C of Nostoc Sp Cytochrome C6
(pdb code 4h0j). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Mutant M58C of Nostoc Sp Cytochrome C6, PDB code: 4h0j:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4h0j
Go back to
Iron Binding Sites List in 4h0j
Iron binding site 1 out
of 6 in the Mutant M58C of Nostoc Sp Cytochrome C6
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Mutant M58C of Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe200
b:20.4
occ:1.00
|
FE
|
A:HEM200
|
0.0
|
20.4
|
1.0
|
|
ND
|
A:HEM200
|
1.9
|
18.7
|
1.0
|
|
NA
|
A:HEM200
|
2.0
|
19.8
|
1.0
|
|
NC
|
A:HEM200
|
2.1
|
19.4
|
1.0
|
|
NB
|
A:HEM200
|
2.1
|
17.6
|
1.0
|
|
NE2
|
A:HIS18
|
2.1
|
14.8
|
1.0
|
|
C1D
|
A:HEM200
|
2.9
|
19.5
|
1.0
|
|
C4D
|
A:HEM200
|
2.9
|
19.2
|
1.0
|
|
C4A
|
A:HEM200
|
3.0
|
19.2
|
1.0
|
|
C1A
|
A:HEM200
|
3.0
|
18.6
|
1.0
|
|
C4C
|
A:HEM200
|
3.0
|
18.4
|
1.0
|
|
C4B
|
A:HEM200
|
3.0
|
18.0
|
1.0
|
|
C1B
|
A:HEM200
|
3.1
|
17.3
|
1.0
|
|
CE1
|
A:HIS18
|
3.1
|
14.9
|
1.0
|
|
C1C
|
A:HEM200
|
3.1
|
20.4
|
1.0
|
|
CD2
|
A:HIS18
|
3.2
|
14.5
|
1.0
|
|
SG
|
A:CYS58
|
3.2
|
26.5
|
1.0
|
|
CHD
|
A:HEM200
|
3.3
|
20.2
|
1.0
|
|
CHA
|
A:HEM200
|
3.3
|
18.4
|
1.0
|
|
CHB
|
A:HEM200
|
3.4
|
18.9
|
1.0
|
|
CHC
|
A:HEM200
|
3.5
|
18.8
|
1.0
|
|
CB
|
A:CYS58
|
4.2
|
24.8
|
1.0
|
|
C2D
|
A:HEM200
|
4.2
|
20.6
|
1.0
|
|
C2A
|
A:HEM200
|
4.2
|
19.3
|
1.0
|
|
C3A
|
A:HEM200
|
4.2
|
19.1
|
1.0
|
|
C3D
|
A:HEM200
|
4.2
|
21.2
|
1.0
|
|
ND1
|
A:HIS18
|
4.2
|
14.8
|
1.0
|
|
C3C
|
A:HEM200
|
4.3
|
18.3
|
1.0
|
|
CG
|
A:HIS18
|
4.3
|
14.7
|
1.0
|
|
C2C
|
A:HEM200
|
4.3
|
19.3
|
1.0
|
|
C2B
|
A:HEM200
|
4.3
|
18.0
|
1.0
|
|
C3B
|
A:HEM200
|
4.3
|
18.2
|
1.0
|
|
CA
|
A:CYS58
|
4.6
|
25.4
|
1.0
|
|
CD
|
A:PRO59
|
5.0
|
25.6
|
1.0
|
|
Iron binding site 2 out
of 6 in 4h0j
Go back to
Iron Binding Sites List in 4h0j
Iron binding site 2 out
of 6 in the Mutant M58C of Nostoc Sp Cytochrome C6
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Mutant M58C of Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe200
b:22.7
occ:1.00
|
FE
|
B:HEM200
|
0.0
|
22.7
|
1.0
|
|
ND
|
B:HEM200
|
1.9
|
22.5
|
1.0
|
|
NA
|
B:HEM200
|
2.0
|
23.7
|
1.0
|
|
NC
|
B:HEM200
|
2.1
|
22.0
|
1.0
|
|
NB
|
B:HEM200
|
2.1
|
22.5
|
1.0
|
|
NE2
|
B:HIS18
|
2.2
|
16.6
|
1.0
|
|
C1D
|
B:HEM200
|
2.9
|
21.7
|
1.0
|
|
C4D
|
B:HEM200
|
2.9
|
23.1
|
1.0
|
|
C1A
|
B:HEM200
|
3.0
|
24.4
|
1.0
|
|
C4B
|
B:HEM200
|
3.0
|
22.6
|
1.0
|
|
C4A
|
B:HEM200
|
3.0
|
22.6
|
1.0
|
|
C1C
|
B:HEM200
|
3.0
|
21.2
|
1.0
|
|
C4C
|
B:HEM200
|
3.0
|
20.7
|
1.0
|
|
C1B
|
B:HEM200
|
3.1
|
22.0
|
1.0
|
|
CE1
|
B:HIS18
|
3.1
|
17.2
|
1.0
|
|
CD2
|
B:HIS18
|
3.2
|
16.5
|
1.0
|
|
CHC
|
B:HEM200
|
3.3
|
22.5
|
1.0
|
|
SG
|
B:CYS58
|
3.3
|
23.9
|
1.0
|
|
CHD
|
B:HEM200
|
3.4
|
22.6
|
1.0
|
|
CHA
|
B:HEM200
|
3.4
|
25.0
|
1.0
|
|
CHB
|
B:HEM200
|
3.4
|
23.0
|
1.0
|
|
C2D
|
B:HEM200
|
4.1
|
21.6
|
1.0
|
|
CB
|
B:CYS58
|
4.1
|
21.3
|
1.0
|
|
C3D
|
B:HEM200
|
4.2
|
23.5
|
1.0
|
|
C2A
|
B:HEM200
|
4.2
|
24.5
|
1.0
|
|
C3A
|
B:HEM200
|
4.2
|
22.3
|
1.0
|
|
C2C
|
B:HEM200
|
4.3
|
20.1
|
1.0
|
|
C3C
|
B:HEM200
|
4.3
|
20.1
|
1.0
|
|
ND1
|
B:HIS18
|
4.3
|
16.9
|
1.0
|
|
CG
|
B:HIS18
|
4.3
|
16.8
|
1.0
|
|
C3B
|
B:HEM200
|
4.3
|
22.5
|
1.0
|
|
C2B
|
B:HEM200
|
4.3
|
23.9
|
1.0
|
|
CA
|
B:CYS58
|
4.5
|
21.1
|
1.0
|
|
CD
|
B:PRO59
|
4.8
|
22.2
|
1.0
|
|
Iron binding site 3 out
of 6 in 4h0j
Go back to
Iron Binding Sites List in 4h0j
Iron binding site 3 out
of 6 in the Mutant M58C of Nostoc Sp Cytochrome C6
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Mutant M58C of Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe200
b:22.9
occ:1.00
|
FE
|
C:HEM200
|
0.0
|
22.9
|
1.0
|
|
ND
|
C:HEM200
|
1.9
|
18.9
|
1.0
|
|
NA
|
C:HEM200
|
2.0
|
22.7
|
1.0
|
|
NB
|
C:HEM200
|
2.1
|
21.4
|
1.0
|
|
NC
|
C:HEM200
|
2.1
|
21.3
|
1.0
|
|
NE2
|
C:HIS18
|
2.2
|
15.4
|
1.0
|
|
C1D
|
C:HEM200
|
2.9
|
19.5
|
1.0
|
|
C4D
|
C:HEM200
|
3.0
|
22.2
|
1.0
|
|
C4A
|
C:HEM200
|
3.0
|
21.1
|
1.0
|
|
C1A
|
C:HEM200
|
3.0
|
20.8
|
1.0
|
|
C4C
|
C:HEM200
|
3.0
|
20.1
|
1.0
|
|
C4B
|
C:HEM200
|
3.0
|
22.0
|
1.0
|
|
C1B
|
C:HEM200
|
3.0
|
21.4
|
1.0
|
|
C1C
|
C:HEM200
|
3.1
|
21.3
|
1.0
|
|
CE1
|
C:HIS18
|
3.1
|
15.7
|
1.0
|
|
CD2
|
C:HIS18
|
3.2
|
15.8
|
1.0
|
|
SG
|
C:CYS58
|
3.3
|
25.8
|
1.0
|
|
CHD
|
C:HEM200
|
3.4
|
21.7
|
1.0
|
|
CHB
|
C:HEM200
|
3.4
|
22.7
|
1.0
|
|
CHA
|
C:HEM200
|
3.4
|
24.2
|
1.0
|
|
CHC
|
C:HEM200
|
3.4
|
21.8
|
1.0
|
|
CB
|
C:CYS58
|
4.1
|
22.9
|
1.0
|
|
C3A
|
C:HEM200
|
4.2
|
23.0
|
1.0
|
|
C2D
|
C:HEM200
|
4.2
|
21.2
|
1.0
|
|
C2A
|
C:HEM200
|
4.2
|
22.1
|
1.0
|
|
ND1
|
C:HIS18
|
4.3
|
16.5
|
1.0
|
|
C3D
|
C:HEM200
|
4.3
|
21.5
|
1.0
|
|
C3C
|
C:HEM200
|
4.3
|
20.6
|
1.0
|
|
C3B
|
C:HEM200
|
4.3
|
20.9
|
1.0
|
|
C2B
|
C:HEM200
|
4.3
|
21.5
|
1.0
|
|
C2C
|
C:HEM200
|
4.3
|
18.4
|
1.0
|
|
CG
|
C:HIS18
|
4.3
|
16.5
|
1.0
|
|
CA
|
C:CYS58
|
4.5
|
23.3
|
1.0
|
|
CD
|
C:PRO59
|
4.9
|
22.7
|
1.0
|
|
Iron binding site 4 out
of 6 in 4h0j
Go back to
Iron Binding Sites List in 4h0j
Iron binding site 4 out
of 6 in the Mutant M58C of Nostoc Sp Cytochrome C6
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Mutant M58C of Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe200
b:25.0
occ:1.00
|
FE
|
D:HEM200
|
0.0
|
25.0
|
1.0
|
|
ND
|
D:HEM200
|
2.0
|
25.9
|
1.0
|
|
NA
|
D:HEM200
|
2.0
|
27.0
|
1.0
|
|
NC
|
D:HEM200
|
2.1
|
25.6
|
1.0
|
|
NB
|
D:HEM200
|
2.1
|
27.4
|
1.0
|
|
NE2
|
D:HIS18
|
2.2
|
20.4
|
1.0
|
|
C4D
|
D:HEM200
|
3.0
|
25.0
|
1.0
|
|
C1A
|
D:HEM200
|
3.0
|
26.9
|
1.0
|
|
C1D
|
D:HEM200
|
3.0
|
24.2
|
1.0
|
|
C4A
|
D:HEM200
|
3.0
|
27.5
|
1.0
|
|
C4B
|
D:HEM200
|
3.0
|
27.4
|
1.0
|
|
C1C
|
D:HEM200
|
3.1
|
28.1
|
1.0
|
|
C4C
|
D:HEM200
|
3.1
|
25.2
|
1.0
|
|
C1B
|
D:HEM200
|
3.1
|
26.8
|
1.0
|
|
CE1
|
D:HIS18
|
3.1
|
18.6
|
1.0
|
|
CD2
|
D:HIS18
|
3.1
|
20.8
|
1.0
|
|
SG
|
D:CYS58
|
3.2
|
28.4
|
1.0
|
|
CHA
|
D:HEM200
|
3.4
|
24.9
|
1.0
|
|
CHC
|
D:HEM200
|
3.4
|
27.9
|
1.0
|
|
CHD
|
D:HEM200
|
3.4
|
24.9
|
1.0
|
|
CHB
|
D:HEM200
|
3.4
|
28.2
|
1.0
|
|
CB
|
D:CYS58
|
4.1
|
24.8
|
1.0
|
|
C3A
|
D:HEM200
|
4.2
|
26.6
|
1.0
|
|
C2A
|
D:HEM200
|
4.2
|
27.3
|
1.0
|
|
ND1
|
D:HIS18
|
4.2
|
19.8
|
1.0
|
|
C3D
|
D:HEM200
|
4.3
|
23.7
|
1.0
|
|
C2D
|
D:HEM200
|
4.3
|
25.1
|
1.0
|
|
C2C
|
D:HEM200
|
4.3
|
27.8
|
1.0
|
|
CG
|
D:HIS18
|
4.3
|
20.5
|
1.0
|
|
C3C
|
D:HEM200
|
4.3
|
26.2
|
1.0
|
|
C2B
|
D:HEM200
|
4.3
|
26.8
|
1.0
|
|
C3B
|
D:HEM200
|
4.3
|
27.2
|
1.0
|
|
CA
|
D:CYS58
|
4.5
|
25.4
|
1.0
|
|
CD
|
D:PRO59
|
4.9
|
28.5
|
1.0
|
|
Iron binding site 5 out
of 6 in 4h0j
Go back to
Iron Binding Sites List in 4h0j
Iron binding site 5 out
of 6 in the Mutant M58C of Nostoc Sp Cytochrome C6
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Mutant M58C of Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe200
b:24.9
occ:1.00
|
FE
|
E:HEM200
|
0.0
|
24.9
|
1.0
|
|
ND
|
E:HEM200
|
1.9
|
24.4
|
1.0
|
|
NA
|
E:HEM200
|
2.0
|
23.1
|
1.0
|
|
NB
|
E:HEM200
|
2.1
|
20.6
|
1.0
|
|
NC
|
E:HEM200
|
2.1
|
22.0
|
1.0
|
|
NE2
|
E:HIS18
|
2.1
|
20.0
|
1.0
|
|
C1D
|
E:HEM200
|
2.9
|
24.3
|
1.0
|
|
C4D
|
E:HEM200
|
2.9
|
24.4
|
1.0
|
|
C4A
|
E:HEM200
|
3.0
|
23.3
|
1.0
|
|
C1A
|
E:HEM200
|
3.0
|
23.3
|
1.0
|
|
C4B
|
E:HEM200
|
3.0
|
22.4
|
1.0
|
|
C1B
|
E:HEM200
|
3.0
|
22.8
|
1.0
|
|
C4C
|
E:HEM200
|
3.0
|
23.2
|
1.0
|
|
CE1
|
E:HIS18
|
3.1
|
20.9
|
1.0
|
|
CD2
|
E:HIS18
|
3.1
|
19.8
|
1.0
|
|
C1C
|
E:HEM200
|
3.1
|
22.0
|
1.0
|
|
SG
|
E:CYS58
|
3.3
|
27.4
|
1.0
|
|
CHD
|
E:HEM200
|
3.3
|
24.4
|
1.0
|
|
CHB
|
E:HEM200
|
3.4
|
22.8
|
1.0
|
|
CHA
|
E:HEM200
|
3.4
|
25.5
|
1.0
|
|
CHC
|
E:HEM200
|
3.5
|
21.8
|
1.0
|
|
C2D
|
E:HEM200
|
4.1
|
25.9
|
1.0
|
|
CB
|
E:CYS58
|
4.1
|
26.4
|
1.0
|
|
C3D
|
E:HEM200
|
4.2
|
28.4
|
1.0
|
|
C3A
|
E:HEM200
|
4.2
|
23.1
|
1.0
|
|
ND1
|
E:HIS18
|
4.2
|
21.7
|
1.0
|
|
C2A
|
E:HEM200
|
4.2
|
24.3
|
1.0
|
|
CG
|
E:HIS18
|
4.2
|
20.2
|
1.0
|
|
C2B
|
E:HEM200
|
4.3
|
23.4
|
1.0
|
|
C3C
|
E:HEM200
|
4.3
|
23.2
|
1.0
|
|
C3B
|
E:HEM200
|
4.3
|
23.4
|
1.0
|
|
C2C
|
E:HEM200
|
4.3
|
24.4
|
1.0
|
|
CA
|
E:CYS58
|
4.6
|
27.9
|
1.0
|
|
CD
|
E:PRO59
|
4.9
|
28.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 4h0j
Go back to
Iron Binding Sites List in 4h0j
Iron binding site 6 out
of 6 in the Mutant M58C of Nostoc Sp Cytochrome C6
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Mutant M58C of Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe200
b:26.0
occ:1.00
|
FE
|
F:HEM200
|
0.0
|
26.0
|
1.0
|
|
ND
|
F:HEM200
|
2.0
|
29.6
|
1.0
|
|
NA
|
F:HEM200
|
2.0
|
27.7
|
1.0
|
|
NC
|
F:HEM200
|
2.0
|
27.7
|
1.0
|
|
NB
|
F:HEM200
|
2.1
|
24.9
|
1.0
|
|
NE2
|
F:HIS18
|
2.2
|
21.0
|
1.0
|
|
C4D
|
F:HEM200
|
3.0
|
27.6
|
1.0
|
|
C1D
|
F:HEM200
|
3.0
|
25.4
|
1.0
|
|
C4B
|
F:HEM200
|
3.0
|
26.2
|
1.0
|
|
C1A
|
F:HEM200
|
3.0
|
26.4
|
1.0
|
|
C4A
|
F:HEM200
|
3.0
|
26.4
|
1.0
|
|
C1B
|
F:HEM200
|
3.1
|
25.9
|
1.0
|
|
C4C
|
F:HEM200
|
3.1
|
25.5
|
1.0
|
|
C1C
|
F:HEM200
|
3.1
|
26.8
|
1.0
|
|
CE1
|
F:HIS18
|
3.1
|
20.8
|
1.0
|
|
CD2
|
F:HIS18
|
3.2
|
20.9
|
1.0
|
|
SG
|
F:CYS58
|
3.3
|
34.1
|
1.0
|
|
CHC
|
F:HEM200
|
3.4
|
27.3
|
1.0
|
|
CHA
|
F:HEM200
|
3.4
|
26.0
|
1.0
|
|
CHB
|
F:HEM200
|
3.4
|
26.9
|
1.0
|
|
CHD
|
F:HEM200
|
3.4
|
28.2
|
1.0
|
|
CB
|
F:CYS58
|
4.1
|
31.2
|
1.0
|
|
C3A
|
F:HEM200
|
4.2
|
27.4
|
1.0
|
|
C2A
|
F:HEM200
|
4.2
|
26.6
|
1.0
|
|
ND1
|
F:HIS18
|
4.2
|
20.7
|
1.0
|
|
C2D
|
F:HEM200
|
4.2
|
27.8
|
1.0
|
|
C3D
|
F:HEM200
|
4.3
|
28.3
|
1.0
|
|
C3C
|
F:HEM200
|
4.3
|
25.8
|
1.0
|
|
C3B
|
F:HEM200
|
4.3
|
29.1
|
1.0
|
|
C2C
|
F:HEM200
|
4.3
|
24.2
|
1.0
|
|
C2B
|
F:HEM200
|
4.3
|
28.5
|
1.0
|
|
CG
|
F:HIS18
|
4.3
|
21.0
|
1.0
|
|
CA
|
F:CYS58
|
4.5
|
30.6
|
1.0
|
|
CD
|
F:PRO59
|
4.9
|
30.1
|
1.0
|
|
Reference:
N.S.Pannu,
P.Skubak,
M.Ubbink,
D.Cavazzini,
G.L.Rossi.
Mutant M58C of Nostoc Sp. Cytochrome C6 To Be Published.
Page generated: Sun Dec 13 15:35:53 2020
|
