Iron in PDB 3c63: Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination
Protein crystallography data
The structure of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination, PDB code: 3c63
was solved by
F.A.Tezcan,
E.N.Salgado,
R.A.Lewis,
J.Faraone-Mennella,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.24 /
1.75
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.966,
89.899,
49.688,
90.00,
110.30,
90.00
|
R / Rfree (%)
|
19.9 /
24.7
|
Other elements in 3c63:
The structure of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination
(pdb code 3c63). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination, PDB code: 3c63:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3c63
Go back to
Iron Binding Sites List in 3c63
Iron binding site 1 out
of 4 in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination
![](/pictures/FE/pdb/c6/3c63-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/c6/3c63-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe150
b:7.4
occ:1.00
|
FE
|
A:HEM150
|
0.0
|
7.4
|
1.0
|
NB
|
A:HEM150
|
1.9
|
4.7
|
1.0
|
NE2
|
A:HIS102
|
2.0
|
6.3
|
1.0
|
ND
|
A:HEM150
|
2.0
|
5.9
|
1.0
|
NC
|
A:HEM150
|
2.0
|
4.3
|
1.0
|
NA
|
A:HEM150
|
2.0
|
5.3
|
1.0
|
SD
|
A:MET7
|
2.3
|
4.7
|
1.0
|
CE1
|
A:HIS102
|
2.9
|
6.4
|
1.0
|
C4B
|
A:HEM150
|
3.0
|
5.1
|
1.0
|
CD2
|
A:HIS102
|
3.0
|
3.3
|
1.0
|
C1C
|
A:HEM150
|
3.0
|
5.9
|
1.0
|
C1B
|
A:HEM150
|
3.0
|
4.5
|
1.0
|
C4D
|
A:HEM150
|
3.1
|
7.0
|
1.0
|
C1A
|
A:HEM150
|
3.1
|
6.4
|
1.0
|
C4A
|
A:HEM150
|
3.1
|
4.6
|
1.0
|
C1D
|
A:HEM150
|
3.1
|
6.8
|
1.0
|
C4C
|
A:HEM150
|
3.1
|
5.3
|
1.0
|
CHC
|
A:HEM150
|
3.4
|
5.2
|
1.0
|
CE
|
A:MET7
|
3.4
|
6.7
|
1.0
|
CHA
|
A:HEM150
|
3.4
|
8.7
|
1.0
|
CG
|
A:MET7
|
3.5
|
3.4
|
1.0
|
CHB
|
A:HEM150
|
3.5
|
4.3
|
1.0
|
CHD
|
A:HEM150
|
3.5
|
6.0
|
1.0
|
ND1
|
A:HIS102
|
4.1
|
7.2
|
1.0
|
CG
|
A:HIS102
|
4.1
|
5.1
|
1.0
|
CB
|
A:MET7
|
4.2
|
4.0
|
1.0
|
C3B
|
A:HEM150
|
4.2
|
3.3
|
1.0
|
C2B
|
A:HEM150
|
4.2
|
4.6
|
1.0
|
C2C
|
A:HEM150
|
4.3
|
5.8
|
1.0
|
C3D
|
A:HEM150
|
4.3
|
7.4
|
1.0
|
C2A
|
A:HEM150
|
4.3
|
7.6
|
1.0
|
C2D
|
A:HEM150
|
4.3
|
7.3
|
1.0
|
C3A
|
A:HEM150
|
4.4
|
6.3
|
1.0
|
C3C
|
A:HEM150
|
4.4
|
4.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 3c63
Go back to
Iron Binding Sites List in 3c63
Iron binding site 2 out
of 4 in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination
![](/pictures/FE/pdb/c6/3c63-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/c6/3c63-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe150
b:6.6
occ:1.00
|
FE
|
B:HEM150
|
0.0
|
6.6
|
1.0
|
ND
|
B:HEM150
|
1.9
|
4.2
|
1.0
|
NA
|
B:HEM150
|
2.0
|
5.0
|
1.0
|
NB
|
B:HEM150
|
2.0
|
5.8
|
1.0
|
NC
|
B:HEM150
|
2.1
|
3.5
|
1.0
|
NE2
|
B:HIS102
|
2.1
|
4.9
|
1.0
|
SD
|
B:MET7
|
2.3
|
7.0
|
1.0
|
C4D
|
B:HEM150
|
2.9
|
6.2
|
1.0
|
C1D
|
B:HEM150
|
3.0
|
5.3
|
1.0
|
C1A
|
B:HEM150
|
3.0
|
6.1
|
1.0
|
CD2
|
B:HIS102
|
3.0
|
5.4
|
1.0
|
C1B
|
B:HEM150
|
3.0
|
7.7
|
1.0
|
C4B
|
B:HEM150
|
3.0
|
5.6
|
1.0
|
C4A
|
B:HEM150
|
3.0
|
6.5
|
1.0
|
CE1
|
B:HIS102
|
3.1
|
7.0
|
1.0
|
C1C
|
B:HEM150
|
3.1
|
3.7
|
1.0
|
C4C
|
B:HEM150
|
3.1
|
4.4
|
1.0
|
CE
|
B:MET7
|
3.3
|
6.4
|
1.0
|
CHA
|
B:HEM150
|
3.4
|
5.6
|
1.0
|
CHD
|
B:HEM150
|
3.4
|
3.8
|
1.0
|
CHB
|
B:HEM150
|
3.4
|
5.2
|
1.0
|
CHC
|
B:HEM150
|
3.4
|
5.1
|
1.0
|
CG
|
B:MET7
|
3.5
|
2.2
|
1.0
|
C3D
|
B:HEM150
|
4.2
|
5.1
|
1.0
|
CB
|
B:MET7
|
4.2
|
4.7
|
1.0
|
ND1
|
B:HIS102
|
4.2
|
6.1
|
1.0
|
C2D
|
B:HEM150
|
4.2
|
4.4
|
1.0
|
CG
|
B:HIS102
|
4.2
|
6.3
|
1.0
|
C2B
|
B:HEM150
|
4.3
|
5.6
|
1.0
|
C2A
|
B:HEM150
|
4.3
|
6.4
|
1.0
|
C3A
|
B:HEM150
|
4.3
|
5.2
|
1.0
|
C3B
|
B:HEM150
|
4.3
|
5.2
|
1.0
|
C2C
|
B:HEM150
|
4.3
|
2.9
|
1.0
|
C3C
|
B:HEM150
|
4.4
|
3.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 3c63
Go back to
Iron Binding Sites List in 3c63
Iron binding site 3 out
of 4 in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination
![](/pictures/FE/pdb/c6/3c63-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/c6/3c63-FE-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe150
b:19.6
occ:1.00
|
FE
|
C:HEM150
|
0.0
|
19.6
|
1.0
|
NA
|
C:HEM150
|
2.0
|
20.3
|
1.0
|
ND
|
C:HEM150
|
2.0
|
18.6
|
1.0
|
NB
|
C:HEM150
|
2.0
|
17.4
|
1.0
|
NE2
|
C:HIS102
|
2.1
|
15.7
|
1.0
|
NC
|
C:HEM150
|
2.1
|
15.0
|
1.0
|
SD
|
C:MET7
|
2.2
|
18.7
|
1.0
|
CE1
|
C:HIS102
|
3.0
|
17.1
|
1.0
|
C1A
|
C:HEM150
|
3.0
|
22.8
|
1.0
|
C4D
|
C:HEM150
|
3.0
|
20.1
|
1.0
|
C4A
|
C:HEM150
|
3.0
|
20.8
|
1.0
|
C1B
|
C:HEM150
|
3.1
|
18.2
|
1.0
|
C4B
|
C:HEM150
|
3.1
|
18.1
|
1.0
|
C1D
|
C:HEM150
|
3.1
|
18.9
|
1.0
|
CD2
|
C:HIS102
|
3.1
|
17.5
|
1.0
|
C1C
|
C:HEM150
|
3.1
|
16.7
|
1.0
|
C4C
|
C:HEM150
|
3.1
|
16.1
|
1.0
|
CG
|
C:MET7
|
3.3
|
20.9
|
1.0
|
CE
|
C:MET7
|
3.4
|
18.7
|
1.0
|
CHA
|
C:HEM150
|
3.4
|
21.4
|
1.0
|
CHB
|
C:HEM150
|
3.4
|
20.2
|
1.0
|
CHC
|
C:HEM150
|
3.5
|
15.3
|
1.0
|
CHD
|
C:HEM150
|
3.5
|
16.1
|
1.0
|
ND1
|
C:HIS102
|
4.2
|
17.0
|
1.0
|
CB
|
C:MET7
|
4.2
|
19.8
|
1.0
|
CG
|
C:HIS102
|
4.2
|
18.0
|
1.0
|
C2A
|
C:HEM150
|
4.3
|
22.4
|
1.0
|
C3A
|
C:HEM150
|
4.3
|
22.1
|
1.0
|
C3D
|
C:HEM150
|
4.3
|
20.7
|
1.0
|
C2B
|
C:HEM150
|
4.3
|
17.9
|
1.0
|
C2D
|
C:HEM150
|
4.3
|
19.3
|
1.0
|
C3B
|
C:HEM150
|
4.3
|
16.9
|
1.0
|
C2C
|
C:HEM150
|
4.4
|
14.9
|
1.0
|
C3C
|
C:HEM150
|
4.4
|
14.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 3c63
Go back to
Iron Binding Sites List in 3c63
Iron binding site 4 out
of 4 in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination
![](/pictures/FE/pdb/c6/3c63-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/c6/3c63-FE-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe150
b:7.6
occ:1.00
|
FE
|
D:HEM150
|
0.0
|
7.6
|
1.0
|
ND
|
D:HEM150
|
2.0
|
6.1
|
1.0
|
NE2
|
D:HIS102
|
2.0
|
6.6
|
1.0
|
NC
|
D:HEM150
|
2.0
|
7.2
|
1.0
|
NB
|
D:HEM150
|
2.0
|
5.8
|
1.0
|
NA
|
D:HEM150
|
2.0
|
6.3
|
1.0
|
SD
|
D:MET7
|
2.3
|
6.2
|
1.0
|
CE1
|
D:HIS102
|
2.9
|
3.8
|
1.0
|
CD2
|
D:HIS102
|
3.0
|
4.1
|
1.0
|
C1D
|
D:HEM150
|
3.0
|
6.0
|
1.0
|
C1C
|
D:HEM150
|
3.0
|
5.2
|
1.0
|
C4C
|
D:HEM150
|
3.0
|
6.2
|
1.0
|
C4B
|
D:HEM150
|
3.0
|
5.7
|
1.0
|
C4D
|
D:HEM150
|
3.0
|
6.0
|
1.0
|
C4A
|
D:HEM150
|
3.1
|
4.5
|
1.0
|
C1A
|
D:HEM150
|
3.1
|
5.5
|
1.0
|
C1B
|
D:HEM150
|
3.1
|
6.7
|
1.0
|
CHC
|
D:HEM150
|
3.4
|
5.5
|
1.0
|
CHD
|
D:HEM150
|
3.4
|
6.6
|
1.0
|
CE
|
D:MET7
|
3.4
|
4.9
|
1.0
|
CG
|
D:MET7
|
3.4
|
2.5
|
1.0
|
CHB
|
D:HEM150
|
3.5
|
4.7
|
1.0
|
CHA
|
D:HEM150
|
3.5
|
4.5
|
1.0
|
ND1
|
D:HIS102
|
4.1
|
7.9
|
1.0
|
CG
|
D:HIS102
|
4.1
|
5.5
|
1.0
|
CB
|
D:MET7
|
4.2
|
5.4
|
1.0
|
C2D
|
D:HEM150
|
4.2
|
7.0
|
1.0
|
C3D
|
D:HEM150
|
4.2
|
7.1
|
1.0
|
C2C
|
D:HEM150
|
4.3
|
4.7
|
1.0
|
C3C
|
D:HEM150
|
4.3
|
5.1
|
1.0
|
C3B
|
D:HEM150
|
4.3
|
4.9
|
1.0
|
C2A
|
D:HEM150
|
4.3
|
6.8
|
1.0
|
C3A
|
D:HEM150
|
4.3
|
5.2
|
1.0
|
C2B
|
D:HEM150
|
4.3
|
5.3
|
1.0
|
|
Reference:
E.N.Salgado,
R.A.Lewis,
J.Faraone-Mennella,
F.A.Tezcan.
Metal-Mediated Self-Assembly of Protein Superstructures: Influence of Secondary Interactions on Protein Oligomerization and Aggregation. J.Am.Chem.Soc. V. 130 6082 2008.
ISSN: ISSN 0002-7863
PubMed: 18422313
DOI: 10.1021/JA8012177
Page generated: Sun Aug 4 08:15:10 2024
|