Iron in PDB 1ezv: Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment
Enzymatic activity of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment
All present enzymatic activity of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment:
1.10.2.2;
Protein crystallography data
The structure of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment, PDB code: 1ezv
was solved by
C.Hunte,
J.Koepke,
C.Lange,
T.Rossmanith,
H.Michel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
2.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
214.470,
163.920,
147.270,
90.00,
117.50,
90.00
|
R / Rfree (%)
|
22.2 /
25.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment
(pdb code 1ezv). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment, PDB code: 1ezv:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 1ezv
Go back to
Iron Binding Sites List in 1ezv
Iron binding site 1 out
of 5 in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:28.3
occ:1.00
|
FE
|
C:HEM401
|
0.0
|
28.3
|
1.0
|
NE2
|
C:HIS82
|
2.0
|
26.6
|
1.0
|
NA
|
C:HEM401
|
2.0
|
26.2
|
1.0
|
NE2
|
C:HIS183
|
2.0
|
27.2
|
1.0
|
ND
|
C:HEM401
|
2.0
|
28.9
|
1.0
|
NB
|
C:HEM401
|
2.0
|
25.9
|
1.0
|
NC
|
C:HEM401
|
2.0
|
27.1
|
1.0
|
CE1
|
C:HIS183
|
2.9
|
24.3
|
1.0
|
CE1
|
C:HIS82
|
2.9
|
25.6
|
1.0
|
C1A
|
C:HEM401
|
3.0
|
29.4
|
1.0
|
C4D
|
C:HEM401
|
3.0
|
29.6
|
1.0
|
C4B
|
C:HEM401
|
3.0
|
25.6
|
1.0
|
C4A
|
C:HEM401
|
3.0
|
28.1
|
1.0
|
C1C
|
C:HEM401
|
3.1
|
28.8
|
1.0
|
CD2
|
C:HIS82
|
3.1
|
26.7
|
1.0
|
C1D
|
C:HEM401
|
3.1
|
29.8
|
1.0
|
C1B
|
C:HEM401
|
3.1
|
26.1
|
1.0
|
C4C
|
C:HEM401
|
3.1
|
27.4
|
1.0
|
CD2
|
C:HIS183
|
3.1
|
26.3
|
1.0
|
CHA
|
C:HEM401
|
3.4
|
26.0
|
1.0
|
CHC
|
C:HEM401
|
3.4
|
27.5
|
1.0
|
CHB
|
C:HEM401
|
3.5
|
27.3
|
1.0
|
CHD
|
C:HEM401
|
3.5
|
28.8
|
1.0
|
ND1
|
C:HIS82
|
4.1
|
26.7
|
1.0
|
ND1
|
C:HIS183
|
4.1
|
27.3
|
1.0
|
CG
|
C:HIS82
|
4.2
|
31.0
|
1.0
|
CG
|
C:HIS183
|
4.2
|
25.2
|
1.0
|
C2A
|
C:HEM401
|
4.2
|
26.0
|
1.0
|
C3A
|
C:HEM401
|
4.3
|
24.4
|
1.0
|
C3D
|
C:HEM401
|
4.3
|
28.3
|
1.0
|
C3B
|
C:HEM401
|
4.3
|
28.5
|
1.0
|
C2C
|
C:HEM401
|
4.3
|
27.1
|
1.0
|
C2D
|
C:HEM401
|
4.3
|
29.1
|
1.0
|
C2B
|
C:HEM401
|
4.3
|
26.6
|
1.0
|
C3C
|
C:HEM401
|
4.3
|
27.9
|
1.0
|
CA
|
C:GLY131
|
4.7
|
31.2
|
1.0
|
|
Iron binding site 2 out
of 5 in 1ezv
Go back to
Iron Binding Sites List in 1ezv
Iron binding site 2 out
of 5 in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:28.7
occ:1.00
|
FE
|
C:HEM402
|
0.0
|
28.7
|
1.0
|
ND
|
C:HEM402
|
2.0
|
31.0
|
1.0
|
NE2
|
C:HIS96
|
2.0
|
27.8
|
1.0
|
NE2
|
C:HIS197
|
2.0
|
28.3
|
1.0
|
NA
|
C:HEM402
|
2.0
|
29.8
|
1.0
|
NC
|
C:HEM402
|
2.0
|
31.4
|
1.0
|
NB
|
C:HEM402
|
2.1
|
31.4
|
1.0
|
CE1
|
C:HIS197
|
2.9
|
28.4
|
1.0
|
CE1
|
C:HIS96
|
3.0
|
28.0
|
1.0
|
C1D
|
C:HEM402
|
3.0
|
29.8
|
1.0
|
CD2
|
C:HIS96
|
3.0
|
27.6
|
1.0
|
C4D
|
C:HEM402
|
3.0
|
31.9
|
1.0
|
C4C
|
C:HEM402
|
3.0
|
29.8
|
1.0
|
C1A
|
C:HEM402
|
3.1
|
30.1
|
1.0
|
C4A
|
C:HEM402
|
3.1
|
28.7
|
1.0
|
CD2
|
C:HIS197
|
3.1
|
26.7
|
1.0
|
C1B
|
C:HEM402
|
3.1
|
29.6
|
1.0
|
C1C
|
C:HEM402
|
3.1
|
32.5
|
1.0
|
C4B
|
C:HEM402
|
3.1
|
32.0
|
1.0
|
CHD
|
C:HEM402
|
3.4
|
31.5
|
1.0
|
CHA
|
C:HEM402
|
3.4
|
30.2
|
1.0
|
CHB
|
C:HEM402
|
3.4
|
27.2
|
1.0
|
CHC
|
C:HEM402
|
3.5
|
29.9
|
1.0
|
ND1
|
C:HIS197
|
4.1
|
27.1
|
1.0
|
ND1
|
C:HIS96
|
4.1
|
25.1
|
1.0
|
CG
|
C:HIS96
|
4.2
|
26.7
|
1.0
|
CG
|
C:HIS197
|
4.2
|
29.7
|
1.0
|
C2D
|
C:HEM402
|
4.2
|
31.6
|
1.0
|
C3D
|
C:HEM402
|
4.2
|
33.1
|
1.0
|
C2A
|
C:HEM402
|
4.3
|
28.8
|
1.0
|
C3C
|
C:HEM402
|
4.3
|
31.6
|
1.0
|
C3A
|
C:HEM402
|
4.3
|
29.8
|
1.0
|
C2C
|
C:HEM402
|
4.3
|
32.1
|
1.0
|
C2B
|
C:HEM402
|
4.3
|
30.7
|
1.0
|
C3B
|
C:HEM402
|
4.3
|
31.2
|
1.0
|
O
|
C:HOH515
|
4.8
|
36.8
|
1.0
|
|
Iron binding site 3 out
of 5 in 1ezv
Go back to
Iron Binding Sites List in 1ezv
Iron binding site 3 out
of 5 in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe3
b:49.0
occ:1.00
|
FE
|
D:HEM3
|
0.0
|
49.0
|
1.0
|
NE2
|
D:HIS105
|
2.0
|
51.3
|
1.0
|
ND
|
D:HEM3
|
2.0
|
46.6
|
1.0
|
NB
|
D:HEM3
|
2.0
|
48.1
|
1.0
|
NC
|
D:HEM3
|
2.0
|
51.1
|
1.0
|
NA
|
D:HEM3
|
2.0
|
47.6
|
1.0
|
SD
|
D:MET225
|
2.2
|
53.5
|
1.0
|
CE1
|
D:HIS105
|
3.0
|
53.9
|
1.0
|
CD2
|
D:HIS105
|
3.0
|
54.2
|
1.0
|
C1D
|
D:HEM3
|
3.0
|
48.5
|
1.0
|
C4D
|
D:HEM3
|
3.0
|
47.7
|
1.0
|
C4C
|
D:HEM3
|
3.0
|
50.2
|
1.0
|
C1B
|
D:HEM3
|
3.1
|
46.7
|
1.0
|
C4B
|
D:HEM3
|
3.1
|
47.3
|
1.0
|
C1C
|
D:HEM3
|
3.1
|
48.1
|
1.0
|
C1A
|
D:HEM3
|
3.1
|
46.5
|
1.0
|
C4A
|
D:HEM3
|
3.1
|
44.6
|
1.0
|
CHD
|
D:HEM3
|
3.4
|
49.3
|
1.0
|
CHA
|
D:HEM3
|
3.4
|
48.1
|
1.0
|
CHC
|
D:HEM3
|
3.4
|
46.7
|
1.0
|
CHB
|
D:HEM3
|
3.4
|
44.7
|
1.0
|
CE
|
D:MET225
|
3.5
|
49.9
|
1.0
|
CG
|
D:MET225
|
3.6
|
51.4
|
1.0
|
ND1
|
D:HIS105
|
4.1
|
54.8
|
1.0
|
CG
|
D:HIS105
|
4.1
|
54.2
|
1.0
|
CB
|
D:MET225
|
4.2
|
53.4
|
1.0
|
C2D
|
D:HEM3
|
4.2
|
48.2
|
1.0
|
C3D
|
D:HEM3
|
4.2
|
47.7
|
1.0
|
C3C
|
D:HEM3
|
4.3
|
51.4
|
1.0
|
C2B
|
D:HEM3
|
4.3
|
46.2
|
1.0
|
C2C
|
D:HEM3
|
4.3
|
50.1
|
1.0
|
C3B
|
D:HEM3
|
4.3
|
47.9
|
1.0
|
C2A
|
D:HEM3
|
4.3
|
45.1
|
1.0
|
C3A
|
D:HEM3
|
4.3
|
45.1
|
1.0
|
|
Iron binding site 4 out
of 5 in 1ezv
Go back to
Iron Binding Sites List in 1ezv
Iron binding site 4 out
of 5 in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe4
b:40.6
occ:1.00
|
FE1
|
E:FES4
|
0.0
|
40.6
|
1.0
|
S1
|
E:FES4
|
2.1
|
36.8
|
1.0
|
S2
|
E:FES4
|
2.2
|
37.8
|
1.0
|
SG
|
E:CYS178
|
2.2
|
41.3
|
1.0
|
SG
|
E:CYS159
|
2.2
|
38.5
|
1.0
|
FE2
|
E:FES4
|
2.9
|
38.0
|
1.0
|
CB
|
E:CYS178
|
3.1
|
41.5
|
1.0
|
CB
|
E:CYS159
|
3.1
|
38.3
|
1.0
|
CB
|
E:HIS161
|
4.1
|
35.0
|
1.0
|
CB
|
E:CYS180
|
4.4
|
36.6
|
1.0
|
CB
|
E:SER183
|
4.5
|
39.2
|
1.0
|
CB
|
E:CYS164
|
4.5
|
36.6
|
1.0
|
OG
|
E:SER183
|
4.5
|
39.0
|
1.0
|
ND1
|
E:HIS161
|
4.5
|
33.5
|
1.0
|
CA
|
E:CYS178
|
4.5
|
40.3
|
1.0
|
N
|
E:HIS181
|
4.5
|
41.6
|
1.0
|
CA
|
E:CYS159
|
4.6
|
38.1
|
1.0
|
ND1
|
E:HIS181
|
4.7
|
36.1
|
1.0
|
N
|
E:LEU162
|
4.8
|
34.4
|
1.0
|
N
|
E:CYS164
|
4.8
|
34.1
|
1.0
|
CG
|
E:HIS161
|
4.8
|
32.5
|
1.0
|
O
|
E:CYS178
|
4.8
|
40.0
|
1.0
|
C
|
E:CYS178
|
4.8
|
40.1
|
1.0
|
C
|
E:CYS159
|
5.0
|
39.8
|
1.0
|
|
Iron binding site 5 out
of 5 in 1ezv
Go back to
Iron Binding Sites List in 1ezv
Iron binding site 5 out
of 5 in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe4
b:38.0
occ:1.00
|
FE2
|
E:FES4
|
0.0
|
38.0
|
1.0
|
ND1
|
E:HIS161
|
2.1
|
33.5
|
1.0
|
ND1
|
E:HIS181
|
2.1
|
36.1
|
1.0
|
S2
|
E:FES4
|
2.2
|
37.8
|
1.0
|
S1
|
E:FES4
|
2.2
|
36.8
|
1.0
|
FE1
|
E:FES4
|
2.9
|
40.6
|
1.0
|
CG
|
E:HIS161
|
3.0
|
32.5
|
1.0
|
CG
|
E:HIS181
|
3.1
|
38.1
|
1.0
|
CE1
|
E:HIS161
|
3.1
|
30.3
|
1.0
|
CE1
|
E:HIS181
|
3.1
|
30.7
|
1.0
|
CB
|
E:HIS161
|
3.3
|
35.0
|
1.0
|
CB
|
E:HIS181
|
3.3
|
38.5
|
1.0
|
N
|
E:HIS181
|
3.7
|
41.6
|
1.0
|
N
|
E:LEU162
|
4.0
|
34.4
|
1.0
|
CA
|
E:HIS181
|
4.1
|
41.0
|
1.0
|
CB
|
E:CYS180
|
4.2
|
36.6
|
1.0
|
CD2
|
E:HIS161
|
4.2
|
33.9
|
1.0
|
CD2
|
E:HIS181
|
4.2
|
37.6
|
1.0
|
NE2
|
E:HIS161
|
4.3
|
35.1
|
1.0
|
NE2
|
E:HIS181
|
4.3
|
35.8
|
1.0
|
CB
|
E:LEU162
|
4.3
|
30.0
|
1.0
|
C
|
E:CYS180
|
4.4
|
40.4
|
1.0
|
SG
|
E:CYS159
|
4.5
|
38.5
|
1.0
|
CG
|
E:LEU162
|
4.5
|
30.3
|
1.0
|
CA
|
E:HIS161
|
4.6
|
35.5
|
1.0
|
SG
|
E:CYS178
|
4.6
|
41.3
|
1.0
|
CG
|
E:PRO195
|
4.7
|
40.8
|
1.0
|
CD1
|
E:LEU162
|
4.7
|
25.9
|
1.0
|
CA
|
E:LEU162
|
4.7
|
34.1
|
1.0
|
C
|
E:HIS161
|
4.7
|
35.2
|
1.0
|
C
|
E:HIS181
|
4.8
|
41.2
|
1.0
|
CA
|
E:CYS180
|
4.9
|
39.4
|
1.0
|
|
Reference:
C.Hunte,
J.Koepke,
C.Lange,
T.Rossmanith,
H.Michel.
Structure at 2.3 A Resolution of the Cytochrome Bc(1) Complex From the Yeast Saccharomyces Cerevisiae Co-Crystallized with An Antibody Fv Fragment. Structure Fold.Des. V. 8 669 2000.
ISSN: ISSN 0969-2126
PubMed: 10873857
DOI: 10.1016/S0969-2126(00)00152-0
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