Iron in PDB 4gyd: Nostoc Sp Cytochrome C6
Protein crystallography data
The structure of Nostoc Sp Cytochrome C6, PDB code: 4gyd
was solved by
P.Skubak,
M.Ubbink,
D.Cavazzini,
G.L.Rossi,
N.S.Pannu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
17.48 /
1.80
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.721,
79.803,
80.154,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.9 /
21.6
|
Iron Binding Sites:
The binding sites of Iron atom in the Nostoc Sp Cytochrome C6
(pdb code 4gyd). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Nostoc Sp Cytochrome C6, PDB code: 4gyd:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4gyd
Go back to
Iron Binding Sites List in 4gyd
Iron binding site 1 out
of 6 in the 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 Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe200
b:10.5
occ:1.00
|
FE
|
A:HEM200
|
0.0
|
10.5
|
1.0
|
|
ND
|
A:HEM200
|
2.0
|
9.1
|
1.0
|
|
NA
|
A:HEM200
|
2.0
|
8.1
|
1.0
|
|
NB
|
A:HEM200
|
2.0
|
8.3
|
1.0
|
|
NE2
|
A:HIS18
|
2.0
|
7.4
|
1.0
|
|
NC
|
A:HEM200
|
2.1
|
10.0
|
1.0
|
|
SD
|
A:MET58
|
2.4
|
12.9
|
1.0
|
|
C4D
|
A:HEM200
|
3.0
|
10.0
|
1.0
|
|
C1D
|
A:HEM200
|
3.0
|
10.0
|
1.0
|
|
C4B
|
A:HEM200
|
3.0
|
8.6
|
1.0
|
|
C4C
|
A:HEM200
|
3.0
|
10.7
|
1.0
|
|
C1A
|
A:HEM200
|
3.0
|
8.6
|
1.0
|
|
C4A
|
A:HEM200
|
3.0
|
8.0
|
1.0
|
|
CE1
|
A:HIS18
|
3.0
|
8.0
|
1.0
|
|
C1B
|
A:HEM200
|
3.0
|
8.8
|
1.0
|
|
CD2
|
A:HIS18
|
3.0
|
7.7
|
1.0
|
|
C1C
|
A:HEM200
|
3.1
|
9.4
|
1.0
|
|
CHD
|
A:HEM200
|
3.4
|
10.6
|
1.0
|
|
CE
|
A:MET58
|
3.4
|
10.3
|
1.0
|
|
CHA
|
A:HEM200
|
3.4
|
8.3
|
1.0
|
|
CHB
|
A:HEM200
|
3.4
|
7.8
|
1.0
|
|
CHC
|
A:HEM200
|
3.4
|
9.5
|
1.0
|
|
CG
|
A:MET58
|
3.7
|
12.4
|
1.0
|
|
ND1
|
A:HIS18
|
4.1
|
7.6
|
1.0
|
|
CG
|
A:HIS18
|
4.2
|
7.3
|
1.0
|
|
CB
|
A:MET58
|
4.2
|
12.7
|
1.0
|
|
C2D
|
A:HEM200
|
4.2
|
9.7
|
1.0
|
|
C3C
|
A:HEM200
|
4.2
|
10.7
|
1.0
|
|
C2B
|
A:HEM200
|
4.2
|
8.0
|
1.0
|
|
C3A
|
A:HEM200
|
4.3
|
8.2
|
1.0
|
|
C3D
|
A:HEM200
|
4.3
|
10.3
|
1.0
|
|
C2A
|
A:HEM200
|
4.3
|
8.1
|
1.0
|
|
C2C
|
A:HEM200
|
4.3
|
10.3
|
1.0
|
|
C3B
|
A:HEM200
|
4.3
|
8.7
|
1.0
|
|
CA
|
A:MET58
|
4.7
|
13.6
|
1.0
|
|
Iron binding site 2 out
of 6 in 4gyd
Go back to
Iron Binding Sites List in 4gyd
Iron binding site 2 out
of 6 in the 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 Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe200
b:9.1
occ:1.00
|
FE
|
B:HEM200
|
0.0
|
9.1
|
1.0
|
|
ND
|
B:HEM200
|
1.9
|
8.7
|
1.0
|
|
NA
|
B:HEM200
|
2.0
|
9.4
|
1.0
|
|
NE2
|
B:HIS18
|
2.1
|
8.6
|
1.0
|
|
NC
|
B:HEM200
|
2.1
|
8.7
|
1.0
|
|
NB
|
B:HEM200
|
2.1
|
8.7
|
1.0
|
|
SD
|
B:MET58
|
2.3
|
8.6
|
1.0
|
|
C4D
|
B:HEM200
|
3.0
|
8.9
|
1.0
|
|
C1D
|
B:HEM200
|
3.0
|
8.5
|
1.0
|
|
C1A
|
B:HEM200
|
3.0
|
9.3
|
1.0
|
|
C4A
|
B:HEM200
|
3.0
|
8.2
|
1.0
|
|
CD2
|
B:HIS18
|
3.0
|
8.4
|
1.0
|
|
C1B
|
B:HEM200
|
3.0
|
7.8
|
1.0
|
|
CE1
|
B:HIS18
|
3.1
|
8.4
|
1.0
|
|
C4C
|
B:HEM200
|
3.1
|
8.3
|
1.0
|
|
C4B
|
B:HEM200
|
3.1
|
9.2
|
1.0
|
|
C1C
|
B:HEM200
|
3.1
|
8.2
|
1.0
|
|
CHA
|
B:HEM200
|
3.4
|
9.0
|
1.0
|
|
CE
|
B:MET58
|
3.4
|
8.5
|
1.0
|
|
CHD
|
B:HEM200
|
3.4
|
8.8
|
1.0
|
|
CHB
|
B:HEM200
|
3.4
|
7.8
|
1.0
|
|
CG
|
B:MET58
|
3.4
|
10.4
|
1.0
|
|
CHC
|
B:HEM200
|
3.5
|
8.4
|
1.0
|
|
CB
|
B:MET58
|
4.1
|
10.0
|
1.0
|
|
ND1
|
B:HIS18
|
4.2
|
8.7
|
1.0
|
|
CG
|
B:HIS18
|
4.2
|
8.2
|
1.0
|
|
C3D
|
B:HEM200
|
4.2
|
9.8
|
1.0
|
|
C3A
|
B:HEM200
|
4.2
|
8.7
|
1.0
|
|
C2A
|
B:HEM200
|
4.2
|
9.1
|
1.0
|
|
C2D
|
B:HEM200
|
4.2
|
9.2
|
1.0
|
|
C2B
|
B:HEM200
|
4.2
|
8.2
|
1.0
|
|
C2C
|
B:HEM200
|
4.3
|
8.9
|
1.0
|
|
C3C
|
B:HEM200
|
4.3
|
9.1
|
1.0
|
|
C3B
|
B:HEM200
|
4.3
|
8.2
|
1.0
|
|
Iron binding site 3 out
of 6 in 4gyd
Go back to
Iron Binding Sites List in 4gyd
Iron binding site 3 out
of 6 in the 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 Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe200
b:10.1
occ:1.00
|
FE
|
C:HEM200
|
0.0
|
10.1
|
1.0
|
|
ND
|
C:HEM200
|
1.9
|
8.6
|
1.0
|
|
NA
|
C:HEM200
|
2.0
|
9.2
|
1.0
|
|
NB
|
C:HEM200
|
2.1
|
9.8
|
1.0
|
|
NC
|
C:HEM200
|
2.1
|
9.7
|
1.0
|
|
NE2
|
C:HIS18
|
2.1
|
7.8
|
1.0
|
|
SD
|
C:MET58
|
2.3
|
15.9
|
1.0
|
|
C4D
|
C:HEM200
|
3.0
|
8.8
|
1.0
|
|
C1A
|
C:HEM200
|
3.0
|
9.8
|
1.0
|
|
C4A
|
C:HEM200
|
3.0
|
9.6
|
1.0
|
|
C1D
|
C:HEM200
|
3.0
|
8.3
|
1.0
|
|
CE1
|
C:HIS18
|
3.0
|
8.0
|
1.0
|
|
C1B
|
C:HEM200
|
3.0
|
9.0
|
1.0
|
|
C4B
|
C:HEM200
|
3.0
|
9.2
|
1.0
|
|
C4C
|
C:HEM200
|
3.1
|
9.2
|
1.0
|
|
C1C
|
C:HEM200
|
3.1
|
9.0
|
1.0
|
|
CD2
|
C:HIS18
|
3.1
|
8.8
|
1.0
|
|
CHA
|
C:HEM200
|
3.4
|
9.8
|
1.0
|
|
CHB
|
C:HEM200
|
3.4
|
9.0
|
1.0
|
|
CHD
|
C:HEM200
|
3.4
|
8.7
|
1.0
|
|
CHC
|
C:HEM200
|
3.4
|
9.0
|
1.0
|
|
CE
|
C:MET58
|
3.5
|
14.0
|
1.0
|
|
CG
|
C:MET58
|
3.8
|
21.3
|
1.0
|
|
ND1
|
C:HIS18
|
4.1
|
8.5
|
1.0
|
|
CB
|
C:MET58
|
4.2
|
17.0
|
1.0
|
|
C3A
|
C:HEM200
|
4.2
|
10.4
|
1.0
|
|
C2A
|
C:HEM200
|
4.2
|
9.8
|
1.0
|
|
CG
|
C:HIS18
|
4.2
|
8.3
|
1.0
|
|
C2D
|
C:HEM200
|
4.2
|
8.9
|
1.0
|
|
C2B
|
C:HEM200
|
4.2
|
9.2
|
1.0
|
|
C3D
|
C:HEM200
|
4.2
|
8.8
|
1.0
|
|
C2C
|
C:HEM200
|
4.3
|
10.0
|
1.0
|
|
C3C
|
C:HEM200
|
4.3
|
9.7
|
1.0
|
|
C3B
|
C:HEM200
|
4.3
|
9.2
|
1.0
|
|
CA
|
C:MET58
|
4.9
|
16.6
|
1.0
|
|
Iron binding site 4 out
of 6 in 4gyd
Go back to
Iron Binding Sites List in 4gyd
Iron binding site 4 out
of 6 in the 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 Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe200
b:12.5
occ:1.00
|
FE
|
D:HEM200
|
0.0
|
12.5
|
1.0
|
|
ND
|
D:HEM200
|
1.9
|
11.5
|
1.0
|
|
NA
|
D:HEM200
|
2.0
|
11.6
|
1.0
|
|
NE2
|
D:HIS18
|
2.1
|
11.7
|
1.0
|
|
NB
|
D:HEM200
|
2.1
|
12.3
|
1.0
|
|
NC
|
D:HEM200
|
2.1
|
11.9
|
1.0
|
|
SD
|
D:MET58
|
2.4
|
13.6
|
1.0
|
|
C4D
|
D:HEM200
|
3.0
|
11.1
|
1.0
|
|
C1D
|
D:HEM200
|
3.0
|
12.0
|
1.0
|
|
C4A
|
D:HEM200
|
3.0
|
10.9
|
1.0
|
|
C4B
|
D:HEM200
|
3.0
|
13.1
|
1.0
|
|
CD2
|
D:HIS18
|
3.0
|
10.7
|
1.0
|
|
C1A
|
D:HEM200
|
3.0
|
11.3
|
1.0
|
|
C1B
|
D:HEM200
|
3.1
|
12.0
|
1.0
|
|
CE1
|
D:HIS18
|
3.1
|
10.8
|
1.0
|
|
C4C
|
D:HEM200
|
3.1
|
12.8
|
1.0
|
|
C1C
|
D:HEM200
|
3.1
|
12.8
|
1.0
|
|
CE
|
D:MET58
|
3.4
|
14.0
|
1.0
|
|
CHA
|
D:HEM200
|
3.4
|
11.2
|
1.0
|
|
CHB
|
D:HEM200
|
3.4
|
11.8
|
1.0
|
|
CHC
|
D:HEM200
|
3.4
|
13.3
|
1.0
|
|
CHD
|
D:HEM200
|
3.5
|
11.8
|
1.0
|
|
CG
|
D:MET58
|
3.6
|
13.4
|
1.0
|
|
C3A
|
D:HEM200
|
4.1
|
11.1
|
1.0
|
|
ND1
|
D:HIS18
|
4.1
|
12.2
|
1.0
|
|
CG
|
D:HIS18
|
4.2
|
12.1
|
1.0
|
|
C2A
|
D:HEM200
|
4.2
|
11.8
|
1.0
|
|
CB
|
D:MET58
|
4.2
|
13.0
|
1.0
|
|
C2D
|
D:HEM200
|
4.2
|
10.4
|
1.0
|
|
C2B
|
D:HEM200
|
4.3
|
13.1
|
1.0
|
|
C3D
|
D:HEM200
|
4.3
|
10.8
|
1.0
|
|
C3B
|
D:HEM200
|
4.3
|
13.0
|
1.0
|
|
C3C
|
D:HEM200
|
4.3
|
13.1
|
1.0
|
|
C2C
|
D:HEM200
|
4.3
|
12.9
|
1.0
|
|
CA
|
D:MET58
|
4.7
|
14.1
|
1.0
|
|
Iron binding site 5 out
of 6 in 4gyd
Go back to
Iron Binding Sites List in 4gyd
Iron binding site 5 out
of 6 in the 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 Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe200
b:12.2
occ:1.00
|
FE
|
E:HEM200
|
0.0
|
12.2
|
1.0
|
|
ND
|
E:HEM200
|
1.9
|
11.1
|
1.0
|
|
NA
|
E:HEM200
|
2.0
|
10.9
|
1.0
|
|
NB
|
E:HEM200
|
2.0
|
10.5
|
1.0
|
|
NE2
|
E:HIS18
|
2.0
|
10.4
|
1.0
|
|
NC
|
E:HEM200
|
2.1
|
10.9
|
1.0
|
|
SD
|
E:MET58
|
2.4
|
15.3
|
1.0
|
|
C4D
|
E:HEM200
|
2.9
|
11.3
|
1.0
|
|
C1D
|
E:HEM200
|
3.0
|
10.9
|
1.0
|
|
C4B
|
E:HEM200
|
3.0
|
10.4
|
1.0
|
|
C1A
|
E:HEM200
|
3.0
|
11.1
|
1.0
|
|
C4A
|
E:HEM200
|
3.0
|
10.3
|
1.0
|
|
CE1
|
E:HIS18
|
3.0
|
10.6
|
1.0
|
|
CD2
|
E:HIS18
|
3.0
|
9.6
|
1.0
|
|
C4C
|
E:HEM200
|
3.1
|
10.1
|
1.0
|
|
C1B
|
E:HEM200
|
3.1
|
10.0
|
1.0
|
|
C1C
|
E:HEM200
|
3.1
|
10.6
|
1.0
|
|
CHA
|
E:HEM200
|
3.3
|
10.5
|
1.0
|
|
CHD
|
E:HEM200
|
3.4
|
10.5
|
1.0
|
|
CHB
|
E:HEM200
|
3.4
|
10.1
|
1.0
|
|
CHC
|
E:HEM200
|
3.4
|
10.7
|
1.0
|
|
CE
|
E:MET58
|
3.5
|
12.2
|
1.0
|
|
CG
|
E:MET58
|
3.7
|
14.7
|
1.0
|
|
ND1
|
E:HIS18
|
4.1
|
10.2
|
1.0
|
|
CG
|
E:HIS18
|
4.2
|
10.5
|
1.0
|
|
C3A
|
E:HEM200
|
4.2
|
10.9
|
1.0
|
|
C2A
|
E:HEM200
|
4.2
|
11.4
|
1.0
|
|
C3D
|
E:HEM200
|
4.2
|
11.5
|
1.0
|
|
C2D
|
E:HEM200
|
4.2
|
11.4
|
1.0
|
|
CB
|
E:MET58
|
4.2
|
12.9
|
1.0
|
|
C3B
|
E:HEM200
|
4.3
|
10.7
|
1.0
|
|
C3C
|
E:HEM200
|
4.3
|
9.9
|
1.0
|
|
C2C
|
E:HEM200
|
4.3
|
9.7
|
1.0
|
|
C2B
|
E:HEM200
|
4.3
|
9.8
|
1.0
|
|
CA
|
E:MET58
|
4.8
|
12.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 4gyd
Go back to
Iron Binding Sites List in 4gyd
Iron binding site 6 out
of 6 in the 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 Nostoc Sp Cytochrome C6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe200
b:11.3
occ:1.00
|
FE
|
F:HEM200
|
0.0
|
11.3
|
1.0
|
|
ND
|
F:HEM200
|
2.0
|
10.1
|
1.0
|
|
NA
|
F:HEM200
|
2.0
|
10.2
|
1.0
|
|
NC
|
F:HEM200
|
2.0
|
10.3
|
1.0
|
|
NB
|
F:HEM200
|
2.1
|
10.5
|
1.0
|
|
NE2
|
F:HIS18
|
2.1
|
10.4
|
1.0
|
|
SD
|
F:MET58
|
2.3
|
14.2
|
1.0
|
|
C1D
|
F:HEM200
|
3.0
|
9.1
|
1.0
|
|
C4D
|
F:HEM200
|
3.0
|
9.6
|
1.0
|
|
C1A
|
F:HEM200
|
3.0
|
10.3
|
1.0
|
|
C4B
|
F:HEM200
|
3.0
|
10.9
|
1.0
|
|
C4A
|
F:HEM200
|
3.0
|
10.3
|
1.0
|
|
C1B
|
F:HEM200
|
3.0
|
10.3
|
1.0
|
|
C4C
|
F:HEM200
|
3.0
|
9.1
|
1.0
|
|
CD2
|
F:HIS18
|
3.0
|
10.3
|
1.0
|
|
C1C
|
F:HEM200
|
3.1
|
10.4
|
1.0
|
|
CE1
|
F:HIS18
|
3.1
|
10.3
|
1.0
|
|
CG
|
F:MET58
|
3.3
|
12.8
|
1.0
|
|
CHC
|
F:HEM200
|
3.4
|
9.7
|
1.0
|
|
CHD
|
F:HEM200
|
3.4
|
10.0
|
1.0
|
|
CHA
|
F:HEM200
|
3.4
|
9.9
|
1.0
|
|
CE
|
F:MET58
|
3.4
|
12.2
|
1.0
|
|
CHB
|
F:HEM200
|
3.4
|
9.7
|
1.0
|
|
CB
|
F:MET58
|
4.0
|
14.4
|
1.0
|
|
ND1
|
F:HIS18
|
4.2
|
10.8
|
1.0
|
|
CG
|
F:HIS18
|
4.2
|
9.8
|
1.0
|
|
C3A
|
F:HEM200
|
4.2
|
10.6
|
1.0
|
|
C2D
|
F:HEM200
|
4.2
|
9.4
|
1.0
|
|
C2A
|
F:HEM200
|
4.2
|
10.1
|
1.0
|
|
C3D
|
F:HEM200
|
4.2
|
9.2
|
1.0
|
|
C2B
|
F:HEM200
|
4.3
|
10.6
|
1.0
|
|
C2C
|
F:HEM200
|
4.3
|
10.1
|
1.0
|
|
C3C
|
F:HEM200
|
4.3
|
9.4
|
1.0
|
|
C3B
|
F:HEM200
|
4.3
|
10.7
|
1.0
|
|
CA
|
F:MET58
|
5.0
|
14.4
|
1.0
|
|
Reference:
P.Skubak,
M.Ubbink,
D.Cavazzini,
G.L.Rossi,
N.S.Pannu.
Cytochrome C6 From Nostoc Sp To Be Published.
Page generated: Mon Aug 5 03:05:01 2024
|
