Iron in PDB 3de8: Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination
Protein crystallography data
The structure of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination, PDB code: 3de8
was solved by
E.N.Salgado,
R.A.Lewis,
A.L.Rheingold,
F.A.Tezcan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.92 /
1.72
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.566,
89.504,
52.019,
90.00,
111.01,
90.00
|
R / Rfree (%)
|
19.4 /
24.4
|
Other elements in 3de8:
The structure of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination
(pdb code 3de8). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination, PDB code: 3de8:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3de8
Go back to
Iron Binding Sites List in 3de8
Iron binding site 1 out
of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination
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 A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe150
b:12.7
occ:1.00
|
FE
|
A:HEM150
|
0.0
|
12.7
|
1.0
|
NA
|
A:HEM150
|
2.0
|
10.7
|
1.0
|
NB
|
A:HEM150
|
2.0
|
11.1
|
1.0
|
NC
|
A:HEM150
|
2.0
|
9.8
|
1.0
|
NE2
|
A:HIS102
|
2.1
|
22.8
|
1.0
|
ND
|
A:HEM150
|
2.1
|
12.8
|
1.0
|
SD
|
A:MET7
|
2.3
|
21.6
|
1.0
|
CE1
|
A:HIS102
|
3.0
|
19.8
|
1.0
|
C1A
|
A:HEM150
|
3.0
|
15.8
|
1.0
|
C4A
|
A:HEM150
|
3.0
|
13.3
|
1.0
|
C4B
|
A:HEM150
|
3.1
|
12.7
|
1.0
|
C1C
|
A:HEM150
|
3.1
|
12.0
|
1.0
|
C4D
|
A:HEM150
|
3.1
|
13.2
|
1.0
|
CD2
|
A:HIS102
|
3.1
|
20.1
|
1.0
|
C1B
|
A:HEM150
|
3.1
|
12.6
|
1.0
|
C1D
|
A:HEM150
|
3.1
|
13.5
|
1.0
|
C4C
|
A:HEM150
|
3.1
|
12.5
|
1.0
|
CE
|
A:MET7
|
3.3
|
20.6
|
1.0
|
CG
|
A:MET7
|
3.4
|
19.1
|
1.0
|
CHA
|
A:HEM150
|
3.4
|
13.7
|
1.0
|
CHB
|
A:HEM150
|
3.4
|
13.8
|
1.0
|
CHC
|
A:HEM150
|
3.4
|
13.6
|
1.0
|
CHD
|
A:HEM150
|
3.5
|
13.8
|
1.0
|
ND1
|
A:HIS102
|
4.2
|
24.1
|
1.0
|
CG
|
A:HIS102
|
4.2
|
21.7
|
1.0
|
CB
|
A:MET7
|
4.2
|
19.1
|
1.0
|
C3A
|
A:HEM150
|
4.3
|
14.7
|
1.0
|
C2B
|
A:HEM150
|
4.3
|
11.5
|
1.0
|
C3B
|
A:HEM150
|
4.3
|
11.3
|
1.0
|
C2A
|
A:HEM150
|
4.3
|
13.8
|
1.0
|
C2C
|
A:HEM150
|
4.3
|
11.4
|
1.0
|
C3D
|
A:HEM150
|
4.3
|
15.8
|
1.0
|
C3C
|
A:HEM150
|
4.3
|
11.3
|
1.0
|
C2D
|
A:HEM150
|
4.3
|
12.9
|
1.0
|
NH2
|
A:ARG106
|
4.9
|
29.0
|
1.0
|
|
Iron binding site 2 out
of 4 in 3de8
Go back to
Iron Binding Sites List in 3de8
Iron binding site 2 out
of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination
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 A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe150
b:12.3
occ:1.00
|
FE
|
B:HEM150
|
0.0
|
12.3
|
1.0
|
NB
|
B:HEM150
|
2.0
|
11.4
|
1.0
|
NC
|
B:HEM150
|
2.0
|
11.3
|
1.0
|
NE2
|
B:HIS102
|
2.0
|
18.0
|
1.0
|
NA
|
B:HEM150
|
2.0
|
12.2
|
1.0
|
ND
|
B:HEM150
|
2.1
|
11.2
|
1.0
|
SD
|
B:MET7
|
2.3
|
21.4
|
1.0
|
CE1
|
B:HIS102
|
3.0
|
20.6
|
1.0
|
CD2
|
B:HIS102
|
3.0
|
19.7
|
1.0
|
C1C
|
B:HEM150
|
3.0
|
10.4
|
1.0
|
C4B
|
B:HEM150
|
3.0
|
11.2
|
1.0
|
C4A
|
B:HEM150
|
3.0
|
13.1
|
1.0
|
C1B
|
B:HEM150
|
3.1
|
11.3
|
1.0
|
C4C
|
B:HEM150
|
3.1
|
11.3
|
1.0
|
C1A
|
B:HEM150
|
3.1
|
14.6
|
1.0
|
C1D
|
B:HEM150
|
3.1
|
11.7
|
1.0
|
C4D
|
B:HEM150
|
3.1
|
11.4
|
1.0
|
CG
|
B:MET7
|
3.3
|
20.6
|
1.0
|
CE
|
B:MET7
|
3.4
|
20.4
|
1.0
|
CHC
|
B:HEM150
|
3.4
|
10.6
|
1.0
|
CHB
|
B:HEM150
|
3.4
|
13.2
|
1.0
|
CHA
|
B:HEM150
|
3.4
|
13.1
|
1.0
|
CHD
|
B:HEM150
|
3.4
|
12.1
|
1.0
|
ND1
|
B:HIS102
|
4.1
|
19.7
|
1.0
|
CB
|
B:MET7
|
4.1
|
21.5
|
1.0
|
CG
|
B:HIS102
|
4.2
|
20.4
|
1.0
|
C2B
|
B:HEM150
|
4.3
|
8.7
|
1.0
|
C2C
|
B:HEM150
|
4.3
|
11.1
|
1.0
|
C3B
|
B:HEM150
|
4.3
|
10.1
|
1.0
|
C3A
|
B:HEM150
|
4.3
|
15.8
|
1.0
|
C2A
|
B:HEM150
|
4.3
|
16.2
|
1.0
|
C3C
|
B:HEM150
|
4.3
|
10.5
|
1.0
|
C2D
|
B:HEM150
|
4.3
|
11.4
|
1.0
|
C3D
|
B:HEM150
|
4.3
|
11.3
|
1.0
|
CA
|
B:MET7
|
4.9
|
20.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 3de8
Go back to
Iron Binding Sites List in 3de8
Iron binding site 3 out
of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination
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 A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe150
b:17.8
occ:1.00
|
FE
|
C:HEM150
|
0.0
|
17.8
|
1.0
|
NE2
|
C:HIS102
|
2.0
|
18.6
|
1.0
|
NC
|
C:HEM150
|
2.0
|
18.0
|
1.0
|
ND
|
C:HEM150
|
2.1
|
17.7
|
1.0
|
NA
|
C:HEM150
|
2.1
|
19.8
|
1.0
|
NB
|
C:HEM150
|
2.1
|
17.4
|
1.0
|
SD
|
C:MET7
|
2.3
|
20.7
|
1.0
|
CE1
|
C:HIS102
|
3.0
|
19.4
|
1.0
|
C4C
|
C:HEM150
|
3.0
|
17.4
|
1.0
|
C1C
|
C:HEM150
|
3.0
|
17.7
|
1.0
|
CD2
|
C:HIS102
|
3.0
|
21.6
|
1.0
|
C4B
|
C:HEM150
|
3.1
|
17.8
|
1.0
|
C4A
|
C:HEM150
|
3.1
|
19.2
|
1.0
|
C1A
|
C:HEM150
|
3.1
|
21.4
|
1.0
|
C1D
|
C:HEM150
|
3.1
|
17.0
|
1.0
|
C4D
|
C:HEM150
|
3.1
|
18.7
|
1.0
|
C1B
|
C:HEM150
|
3.1
|
17.7
|
1.0
|
CE
|
C:MET7
|
3.3
|
23.0
|
1.0
|
CG
|
C:MET7
|
3.4
|
21.5
|
1.0
|
CHC
|
C:HEM150
|
3.4
|
16.3
|
1.0
|
CHD
|
C:HEM150
|
3.4
|
18.3
|
1.0
|
CHA
|
C:HEM150
|
3.5
|
19.7
|
1.0
|
CHB
|
C:HEM150
|
3.5
|
18.4
|
1.0
|
ND1
|
C:HIS102
|
4.1
|
20.7
|
1.0
|
CG
|
C:HIS102
|
4.2
|
20.3
|
1.0
|
CB
|
C:MET7
|
4.2
|
22.9
|
1.0
|
C2C
|
C:HEM150
|
4.3
|
18.1
|
1.0
|
C3C
|
C:HEM150
|
4.3
|
18.3
|
1.0
|
C3A
|
C:HEM150
|
4.3
|
20.7
|
1.0
|
C2A
|
C:HEM150
|
4.3
|
20.1
|
1.0
|
C3B
|
C:HEM150
|
4.3
|
15.8
|
1.0
|
C2B
|
C:HEM150
|
4.3
|
17.7
|
1.0
|
C3D
|
C:HEM150
|
4.3
|
18.5
|
1.0
|
C2D
|
C:HEM150
|
4.3
|
18.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 3de8
Go back to
Iron Binding Sites List in 3de8
Iron binding site 4 out
of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination
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 A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe150
b:26.8
occ:1.00
|
FE
|
D:HEM150
|
0.0
|
26.8
|
1.0
|
NE2
|
D:HIS102
|
2.0
|
21.5
|
1.0
|
ND
|
D:HEM150
|
2.0
|
29.1
|
1.0
|
NC
|
D:HEM150
|
2.1
|
28.3
|
1.0
|
NA
|
D:HEM150
|
2.1
|
28.2
|
1.0
|
NB
|
D:HEM150
|
2.1
|
26.0
|
1.0
|
SD
|
D:MET7
|
2.5
|
24.1
|
1.0
|
CE1
|
D:HIS102
|
2.9
|
19.7
|
1.0
|
CD2
|
D:HIS102
|
3.0
|
21.1
|
1.0
|
C4D
|
D:HEM150
|
3.1
|
29.9
|
1.0
|
C1D
|
D:HEM150
|
3.1
|
30.1
|
1.0
|
C4C
|
D:HEM150
|
3.1
|
28.9
|
1.0
|
C4A
|
D:HEM150
|
3.1
|
27.9
|
1.0
|
C1B
|
D:HEM150
|
3.1
|
26.0
|
1.0
|
C1A
|
D:HEM150
|
3.1
|
29.6
|
1.0
|
C1C
|
D:HEM150
|
3.1
|
27.9
|
1.0
|
C4B
|
D:HEM150
|
3.1
|
26.3
|
1.0
|
CHA
|
D:HEM150
|
3.4
|
30.6
|
1.0
|
CHD
|
D:HEM150
|
3.4
|
29.1
|
1.0
|
CHB
|
D:HEM150
|
3.4
|
27.2
|
1.0
|
CHC
|
D:HEM150
|
3.5
|
26.7
|
1.0
|
CE
|
D:MET7
|
3.5
|
22.6
|
1.0
|
CG
|
D:MET7
|
3.7
|
23.6
|
1.0
|
ND1
|
D:HIS102
|
4.0
|
19.7
|
1.0
|
CG
|
D:HIS102
|
4.1
|
20.5
|
1.0
|
C2D
|
D:HEM150
|
4.3
|
29.4
|
1.0
|
C3D
|
D:HEM150
|
4.3
|
30.2
|
1.0
|
C3C
|
D:HEM150
|
4.3
|
28.1
|
1.0
|
C3A
|
D:HEM150
|
4.3
|
28.7
|
1.0
|
C2C
|
D:HEM150
|
4.3
|
27.6
|
1.0
|
C2B
|
D:HEM150
|
4.3
|
24.4
|
1.0
|
C3B
|
D:HEM150
|
4.3
|
24.3
|
1.0
|
C2A
|
D:HEM150
|
4.3
|
29.9
|
1.0
|
CB
|
D:MET7
|
4.5
|
23.3
|
1.0
|
NH2
|
D:ARG106
|
4.8
|
28.2
|
1.0
|
O
|
D:CYS98
|
5.0
|
21.9
|
1.0
|
|
Reference:
E.N.Salgado,
R.A.Lewis,
S.Mossin,
A.L.Rheingold,
F.A.Tezcan.
Control of Protein Oligomerization Symmetry By Metal Coordination: C2 and C3 Symmetrical Assemblies Through Cu(II) and Ni(II) Coordination. Inorg.Chem. V. 48 2726 2009.
ISSN: ISSN 0020-1669
PubMed: 19267481
DOI: 10.1021/IC9001237
Page generated: Sun Aug 4 09:05:36 2024
|