Iron in PDB 9l08: Cyclic Trimer of Helix-Linked Cytochrome C555
Protein crystallography data
The structure of Cyclic Trimer of Helix-Linked Cytochrome C555, PDB code: 9l08
was solved by
G.Novientri,
T.Mashima,
H.Matsuura,
H.Ogata,
S.Hirota,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.12 /
1.60
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.704,
104.519,
73.705,
90,
92.95,
90
|
|
R / Rfree (%)
|
17.2 /
21.1
|
Iron Binding Sites:
The binding sites of Iron atom in the Cyclic Trimer of Helix-Linked Cytochrome C555
(pdb code 9l08). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Cyclic Trimer of Helix-Linked Cytochrome C555, PDB code: 9l08:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 9l08
Go back to
Iron Binding Sites List in 9l08
Iron binding site 1 out
of 6 in the Cyclic Trimer of Helix-Linked Cytochrome C555
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cyclic Trimer of Helix-Linked Cytochrome C555 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:16.3
occ:1.00
|
FE
|
A:HEC401
|
0.0
|
16.3
|
1.0
|
|
NE2
|
A:HIS61
|
2.0
|
15.1
|
1.0
|
|
NA
|
A:HEC401
|
2.0
|
16.3
|
1.0
|
|
NB
|
A:HEC401
|
2.0
|
16.2
|
1.0
|
|
NC
|
A:HEC401
|
2.0
|
17.1
|
1.0
|
|
ND
|
A:HEC401
|
2.0
|
17.1
|
1.0
|
|
SD
|
A:MET107
|
2.4
|
16.4
|
1.0
|
|
CD2
|
A:HIS61
|
3.0
|
15.4
|
1.0
|
|
CE1
|
A:HIS61
|
3.0
|
16.2
|
1.0
|
|
C4D
|
A:HEC401
|
3.0
|
16.8
|
1.0
|
|
C4B
|
A:HEC401
|
3.1
|
15.1
|
1.0
|
|
C4C
|
A:HEC401
|
3.1
|
18.1
|
1.0
|
|
C1A
|
A:HEC401
|
3.1
|
16.9
|
1.0
|
|
C1B
|
A:HEC401
|
3.1
|
15.8
|
1.0
|
|
C1D
|
A:HEC401
|
3.1
|
17.5
|
1.0
|
|
C4A
|
A:HEC401
|
3.1
|
15.7
|
1.0
|
|
C1C
|
A:HEC401
|
3.1
|
15.7
|
1.0
|
|
CHA
|
A:HEC401
|
3.4
|
16.9
|
1.0
|
|
CE
|
A:MET107
|
3.4
|
17.6
|
1.0
|
|
CHD
|
A:HEC401
|
3.4
|
18.3
|
1.0
|
|
CHB
|
A:HEC401
|
3.4
|
16.3
|
1.0
|
|
CHC
|
A:HEC401
|
3.4
|
15.4
|
1.0
|
|
CG
|
A:MET107
|
3.5
|
15.2
|
1.0
|
|
ND1
|
A:HIS61
|
4.1
|
18.3
|
1.0
|
|
CG
|
A:HIS61
|
4.1
|
16.9
|
1.0
|
|
CB
|
A:MET107
|
4.2
|
15.9
|
1.0
|
|
C3B
|
A:HEC401
|
4.3
|
15.7
|
1.0
|
|
C2B
|
A:HEC401
|
4.3
|
16.2
|
1.0
|
|
C2C
|
A:HEC401
|
4.3
|
16.2
|
1.0
|
|
C3C
|
A:HEC401
|
4.3
|
16.8
|
1.0
|
|
C3D
|
A:HEC401
|
4.3
|
18.2
|
1.0
|
|
C2A
|
A:HEC401
|
4.3
|
16.9
|
1.0
|
|
C3A
|
A:HEC401
|
4.3
|
15.6
|
1.0
|
|
C2D
|
A:HEC401
|
4.3
|
18.2
|
1.0
|
|
CA
|
A:MET107
|
4.9
|
17.0
|
1.0
|
|
Iron binding site 2 out
of 6 in 9l08
Go back to
Iron Binding Sites List in 9l08
Iron binding site 2 out
of 6 in the Cyclic Trimer of Helix-Linked Cytochrome C555
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cyclic Trimer of Helix-Linked Cytochrome C555 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:18.2
occ:1.00
|
FE
|
A:HEC402
|
0.0
|
18.2
|
1.0
|
|
NE2
|
A:HIS158
|
2.0
|
18.3
|
1.0
|
|
NA
|
A:HEC402
|
2.0
|
17.5
|
1.0
|
|
NC
|
A:HEC402
|
2.0
|
18.0
|
1.0
|
|
ND
|
A:HEC402
|
2.0
|
19.3
|
1.0
|
|
NB
|
A:HEC402
|
2.0
|
18.4
|
1.0
|
|
SD
|
A:MET204
|
2.4
|
18.2
|
1.0
|
|
CE1
|
A:HIS158
|
2.9
|
19.8
|
1.0
|
|
CD2
|
A:HIS158
|
3.0
|
17.4
|
1.0
|
|
C1A
|
A:HEC402
|
3.0
|
18.9
|
1.0
|
|
C4B
|
A:HEC402
|
3.0
|
17.0
|
1.0
|
|
C4D
|
A:HEC402
|
3.0
|
19.0
|
1.0
|
|
C4C
|
A:HEC402
|
3.1
|
18.5
|
1.0
|
|
C1C
|
A:HEC402
|
3.1
|
17.3
|
1.0
|
|
C4A
|
A:HEC402
|
3.1
|
17.2
|
1.0
|
|
C1D
|
A:HEC402
|
3.1
|
19.1
|
1.0
|
|
C1B
|
A:HEC402
|
3.1
|
17.5
|
1.0
|
|
CHA
|
A:HEC402
|
3.4
|
17.3
|
1.0
|
|
CHC
|
A:HEC402
|
3.4
|
15.8
|
1.0
|
|
CE
|
A:MET204
|
3.4
|
18.9
|
1.0
|
|
CHD
|
A:HEC402
|
3.4
|
19.7
|
1.0
|
|
CHB
|
A:HEC402
|
3.5
|
17.3
|
1.0
|
|
CG
|
A:MET204
|
3.5
|
16.7
|
1.0
|
|
ND1
|
A:HIS158
|
4.0
|
20.5
|
1.0
|
|
CG
|
A:HIS158
|
4.1
|
19.2
|
1.0
|
|
CB
|
A:MET204
|
4.2
|
18.0
|
1.0
|
|
C2A
|
A:HEC402
|
4.3
|
20.0
|
1.0
|
|
C3B
|
A:HEC402
|
4.3
|
18.2
|
1.0
|
|
C3A
|
A:HEC402
|
4.3
|
17.7
|
1.0
|
|
C3C
|
A:HEC402
|
4.3
|
19.2
|
1.0
|
|
C2C
|
A:HEC402
|
4.3
|
18.4
|
1.0
|
|
C3D
|
A:HEC402
|
4.3
|
20.2
|
1.0
|
|
C2D
|
A:HEC402
|
4.3
|
20.6
|
1.0
|
|
C2B
|
A:HEC402
|
4.3
|
18.2
|
1.0
|
|
CA
|
A:MET204
|
4.9
|
19.2
|
1.0
|
|
Iron binding site 3 out
of 6 in 9l08
Go back to
Iron Binding Sites List in 9l08
Iron binding site 3 out
of 6 in the Cyclic Trimer of Helix-Linked Cytochrome C555
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cyclic Trimer of Helix-Linked Cytochrome C555 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe403
b:17.9
occ:1.00
|
FE
|
A:HEC403
|
0.0
|
17.9
|
1.0
|
|
NE2
|
A:HIS255
|
2.0
|
18.2
|
1.0
|
|
NC
|
A:HEC403
|
2.0
|
16.6
|
1.0
|
|
NB
|
A:HEC403
|
2.0
|
16.6
|
1.0
|
|
NA
|
A:HEC403
|
2.0
|
17.8
|
1.0
|
|
ND
|
A:HEC403
|
2.1
|
19.5
|
1.0
|
|
SD
|
A:MET10
|
2.4
|
18.1
|
1.0
|
|
CE1
|
A:HIS255
|
3.0
|
18.9
|
1.0
|
|
CD2
|
A:HIS255
|
3.0
|
19.7
|
1.0
|
|
C1C
|
A:HEC403
|
3.0
|
17.6
|
1.0
|
|
C4B
|
A:HEC403
|
3.0
|
16.8
|
1.0
|
|
C1A
|
A:HEC403
|
3.0
|
18.2
|
1.0
|
|
C1B
|
A:HEC403
|
3.1
|
17.4
|
1.0
|
|
C4D
|
A:HEC403
|
3.1
|
18.9
|
1.0
|
|
C4A
|
A:HEC403
|
3.1
|
17.1
|
1.0
|
|
C4C
|
A:HEC403
|
3.1
|
18.7
|
1.0
|
|
C1D
|
A:HEC403
|
3.1
|
17.2
|
1.0
|
|
CHC
|
A:HEC403
|
3.4
|
16.7
|
1.0
|
|
CE
|
A:MET10
|
3.4
|
18.4
|
1.0
|
|
CHA
|
A:HEC403
|
3.4
|
18.0
|
1.0
|
|
CHB
|
A:HEC403
|
3.4
|
17.4
|
1.0
|
|
CHD
|
A:HEC403
|
3.5
|
19.7
|
1.0
|
|
CG
|
A:MET10
|
3.5
|
17.2
|
1.0
|
|
ND1
|
A:HIS255
|
4.1
|
18.5
|
1.0
|
|
CG
|
A:HIS255
|
4.1
|
19.4
|
1.0
|
|
CB
|
A:MET10
|
4.2
|
19.1
|
1.0
|
|
C2C
|
A:HEC403
|
4.2
|
18.3
|
1.0
|
|
C3B
|
A:HEC403
|
4.2
|
17.6
|
1.0
|
|
C2A
|
A:HEC403
|
4.3
|
17.5
|
1.0
|
|
C2B
|
A:HEC403
|
4.3
|
18.3
|
1.0
|
|
C3A
|
A:HEC403
|
4.3
|
17.4
|
1.0
|
|
C3C
|
A:HEC403
|
4.3
|
19.6
|
1.0
|
|
C3D
|
A:HEC403
|
4.3
|
19.4
|
1.0
|
|
C2D
|
A:HEC403
|
4.3
|
19.3
|
1.0
|
|
CA
|
A:MET10
|
4.9
|
20.9
|
1.0
|
|
Iron binding site 4 out
of 6 in 9l08
Go back to
Iron Binding Sites List in 9l08
Iron binding site 4 out
of 6 in the Cyclic Trimer of Helix-Linked Cytochrome C555
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cyclic Trimer of Helix-Linked Cytochrome C555 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:20.7
occ:1.00
|
FE
|
B:HEC401
|
0.0
|
20.7
|
1.0
|
|
NA
|
B:HEC401
|
2.0
|
21.0
|
1.0
|
|
NE2
|
B:HIS61
|
2.0
|
19.6
|
1.0
|
|
NB
|
B:HEC401
|
2.0
|
18.5
|
1.0
|
|
NC
|
B:HEC401
|
2.0
|
19.8
|
1.0
|
|
ND
|
B:HEC401
|
2.1
|
24.1
|
1.0
|
|
SD
|
B:MET107
|
2.4
|
22.0
|
1.0
|
|
CE1
|
B:HIS61
|
3.0
|
20.8
|
1.0
|
|
C1A
|
B:HEC401
|
3.0
|
22.8
|
1.0
|
|
C4A
|
B:HEC401
|
3.0
|
19.6
|
1.0
|
|
C1B
|
B:HEC401
|
3.0
|
17.9
|
1.0
|
|
C4B
|
B:HEC401
|
3.0
|
15.6
|
1.0
|
|
CD2
|
B:HIS61
|
3.1
|
19.6
|
1.0
|
|
C4D
|
B:HEC401
|
3.1
|
25.8
|
1.0
|
|
C1C
|
B:HEC401
|
3.1
|
18.4
|
1.0
|
|
C4C
|
B:HEC401
|
3.1
|
22.9
|
1.0
|
|
C1D
|
B:HEC401
|
3.1
|
24.9
|
1.0
|
|
CHA
|
B:HEC401
|
3.4
|
24.4
|
1.0
|
|
CHB
|
B:HEC401
|
3.4
|
19.2
|
1.0
|
|
CHC
|
B:HEC401
|
3.4
|
15.8
|
1.0
|
|
CHD
|
B:HEC401
|
3.5
|
24.1
|
1.0
|
|
CE
|
B:MET107
|
3.5
|
20.9
|
1.0
|
|
CG
|
B:MET107
|
3.5
|
22.8
|
1.0
|
|
ND1
|
B:HIS61
|
4.1
|
21.5
|
1.0
|
|
CG
|
B:HIS61
|
4.2
|
20.3
|
1.0
|
|
CB
|
B:MET107
|
4.2
|
25.9
|
1.0
|
|
C3A
|
B:HEC401
|
4.2
|
20.1
|
1.0
|
|
C2A
|
B:HEC401
|
4.2
|
22.4
|
1.0
|
|
C3B
|
B:HEC401
|
4.3
|
15.4
|
1.0
|
|
C2B
|
B:HEC401
|
4.3
|
17.6
|
1.0
|
|
C2C
|
B:HEC401
|
4.3
|
20.0
|
1.0
|
|
C3D
|
B:HEC401
|
4.3
|
28.5
|
1.0
|
|
C3C
|
B:HEC401
|
4.3
|
21.6
|
1.0
|
|
C2D
|
B:HEC401
|
4.3
|
27.7
|
1.0
|
|
CA
|
B:MET107
|
4.9
|
26.9
|
1.0
|
|
Iron binding site 5 out
of 6 in 9l08
Go back to
Iron Binding Sites List in 9l08
Iron binding site 5 out
of 6 in the Cyclic Trimer of Helix-Linked Cytochrome C555
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Cyclic Trimer of Helix-Linked Cytochrome C555 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:22.6
occ:1.00
|
FE
|
B:HEC402
|
0.0
|
22.6
|
1.0
|
|
NE2
|
B:HIS158
|
2.0
|
20.4
|
1.0
|
|
ND
|
B:HEC402
|
2.0
|
24.1
|
1.0
|
|
NC
|
B:HEC402
|
2.0
|
20.7
|
1.0
|
|
NA
|
B:HEC402
|
2.0
|
23.8
|
1.0
|
|
NB
|
B:HEC402
|
2.0
|
20.2
|
1.0
|
|
SD
|
B:MET204
|
2.5
|
25.9
|
1.0
|
|
CE1
|
B:HIS158
|
2.9
|
22.8
|
1.0
|
|
CD2
|
B:HIS158
|
3.0
|
19.3
|
1.0
|
|
C1D
|
B:HEC402
|
3.0
|
26.3
|
1.0
|
|
C4D
|
B:HEC402
|
3.1
|
26.6
|
1.0
|
|
C4B
|
B:HEC402
|
3.1
|
19.0
|
1.0
|
|
C1A
|
B:HEC402
|
3.1
|
25.3
|
1.0
|
|
C4C
|
B:HEC402
|
3.1
|
22.0
|
1.0
|
|
C1C
|
B:HEC402
|
3.1
|
20.4
|
1.0
|
|
C1B
|
B:HEC402
|
3.1
|
19.8
|
1.0
|
|
C4A
|
B:HEC402
|
3.1
|
21.7
|
1.0
|
|
CHD
|
B:HEC402
|
3.4
|
25.8
|
1.0
|
|
CHA
|
B:HEC402
|
3.4
|
26.6
|
1.0
|
|
CHC
|
B:HEC402
|
3.4
|
19.0
|
1.0
|
|
CHB
|
B:HEC402
|
3.5
|
20.6
|
1.0
|
|
CG
|
B:MET204
|
3.5
|
24.8
|
1.0
|
|
CE
|
B:MET204
|
3.5
|
26.9
|
1.0
|
|
ND1
|
B:HIS158
|
4.0
|
22.9
|
1.0
|
|
CG
|
B:HIS158
|
4.1
|
20.9
|
1.0
|
|
CB
|
B:MET204
|
4.1
|
26.3
|
1.0
|
|
C3B
|
B:HEC402
|
4.3
|
19.2
|
1.0
|
|
C2D
|
B:HEC402
|
4.3
|
28.4
|
1.0
|
|
C2C
|
B:HEC402
|
4.3
|
20.2
|
1.0
|
|
C3D
|
B:HEC402
|
4.3
|
28.6
|
1.0
|
|
C2A
|
B:HEC402
|
4.3
|
26.5
|
1.0
|
|
C2B
|
B:HEC402
|
4.3
|
19.9
|
1.0
|
|
C3C
|
B:HEC402
|
4.3
|
21.1
|
1.0
|
|
C3A
|
B:HEC402
|
4.3
|
23.8
|
1.0
|
|
CA
|
B:MET204
|
4.8
|
28.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 9l08
Go back to
Iron Binding Sites List in 9l08
Iron binding site 6 out
of 6 in the Cyclic Trimer of Helix-Linked Cytochrome C555
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Cyclic Trimer of Helix-Linked Cytochrome C555 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe403
b:26.6
occ:1.00
|
FE
|
B:HEC403
|
0.0
|
26.6
|
1.0
|
|
NE2
|
B:HIS255
|
2.0
|
25.0
|
1.0
|
|
NC
|
B:HEC403
|
2.0
|
25.0
|
1.0
|
|
NA
|
B:HEC403
|
2.0
|
25.7
|
1.0
|
|
NB
|
B:HEC403
|
2.0
|
21.9
|
1.0
|
|
ND
|
B:HEC403
|
2.1
|
31.2
|
1.0
|
|
SD
|
B:MET10
|
2.6
|
31.8
|
1.0
|
|
CE1
|
B:HIS255
|
2.9
|
23.8
|
1.0
|
|
CD2
|
B:HIS255
|
3.0
|
22.8
|
1.0
|
|
C1C
|
B:HEC403
|
3.0
|
21.5
|
1.0
|
|
C4A
|
B:HEC403
|
3.0
|
23.1
|
1.0
|
|
C4C
|
B:HEC403
|
3.0
|
29.1
|
1.0
|
|
C1A
|
B:HEC403
|
3.0
|
27.7
|
1.0
|
|
C4B
|
B:HEC403
|
3.1
|
19.6
|
1.0
|
|
C1B
|
B:HEC403
|
3.1
|
19.6
|
1.0
|
|
C1D
|
B:HEC403
|
3.1
|
33.7
|
1.0
|
|
C4D
|
B:HEC403
|
3.1
|
33.1
|
1.0
|
|
CHB
|
B:HEC403
|
3.4
|
19.7
|
1.0
|
|
CHC
|
B:HEC403
|
3.4
|
18.4
|
1.0
|
|
CHA
|
B:HEC403
|
3.4
|
30.5
|
1.0
|
|
CHD
|
B:HEC403
|
3.4
|
31.1
|
1.0
|
|
CG
|
B:MET10
|
3.5
|
32.5
|
1.0
|
|
CE
|
B:MET10
|
3.6
|
29.5
|
1.0
|
|
ND1
|
B:HIS255
|
4.0
|
24.6
|
1.0
|
|
CG
|
B:HIS255
|
4.1
|
23.8
|
1.0
|
|
CB
|
B:MET10
|
4.1
|
33.6
|
1.0
|
|
C2C
|
B:HEC403
|
4.2
|
23.9
|
1.0
|
|
C3A
|
B:HEC403
|
4.2
|
24.9
|
1.0
|
|
C3C
|
B:HEC403
|
4.3
|
27.0
|
1.0
|
|
C2A
|
B:HEC403
|
4.3
|
28.5
|
1.0
|
|
C3B
|
B:HEC403
|
4.3
|
17.5
|
1.0
|
|
C2B
|
B:HEC403
|
4.3
|
19.0
|
1.0
|
|
C2D
|
B:HEC403
|
4.3
|
36.0
|
1.0
|
|
C3D
|
B:HEC403
|
4.3
|
35.6
|
1.0
|
|
CA
|
B:MET10
|
4.9
|
35.2
|
1.0
|
|
Reference:
G.Novientri,
K.Fujiwara,
T.Mashima,
H.Matsuura,
H.Ogata,
T.Uchihashi,
S.Fujii,
Y.Sambongi,
S.Hirota.
Construction of A Cyclic Regular-Triangle Trimer of Cytochrome C 555 with A Central Hole Using Sortase A. Chemistry V. 31 04736 2025.
ISSN: ISSN 0947-6539
PubMed: 40148242
DOI: 10.1002/CHEM.202404736
Page generated: Fri Aug 8 07:10:56 2025
|
