Iron in PDB 2e84: Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
Protein crystallography data
The structure of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion, PDB code: 2e84
was solved by
N.Shibata,
K.Suto,
M.Sato,
Y.Morimoto,
M.Kitamura,
Y.Higuchi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
27.20 /
2.70
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.090,
84.070,
142.670,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
20.4 /
25.9
|
Other elements in 2e84:
The structure of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Iron atom in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
(pdb code 2e84). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the
Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion, PDB code: 2e84:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 16 in 2e84
Go back to
Iron Binding Sites List in 2e84
Iron binding site 1 out
of 16 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
 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 High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1301
b:24.7
occ:1.00
|
FE
|
A:HEM1301
|
0.0
|
24.7
|
1.0
|
|
ND
|
A:HEM1301
|
2.0
|
23.2
|
1.0
|
|
NB
|
A:HEM1301
|
2.0
|
23.0
|
1.0
|
|
NC
|
A:HEM1301
|
2.0
|
30.8
|
1.0
|
|
NA
|
A:HEM1301
|
2.0
|
27.9
|
1.0
|
|
NE2
|
A:HIS66
|
2.2
|
16.2
|
1.0
|
|
NE2
|
A:HIS87
|
2.2
|
33.8
|
1.0
|
|
C4D
|
A:HEM1301
|
3.0
|
26.7
|
1.0
|
|
C1D
|
A:HEM1301
|
3.0
|
29.6
|
1.0
|
|
C1A
|
A:HEM1301
|
3.0
|
27.6
|
1.0
|
|
CD2
|
A:HIS66
|
3.0
|
13.3
|
1.0
|
|
C1B
|
A:HEM1301
|
3.0
|
27.1
|
1.0
|
|
C1C
|
A:HEM1301
|
3.1
|
28.6
|
1.0
|
|
C4A
|
A:HEM1301
|
3.1
|
28.2
|
1.0
|
|
C4C
|
A:HEM1301
|
3.1
|
31.3
|
1.0
|
|
C4B
|
A:HEM1301
|
3.1
|
22.3
|
1.0
|
|
CD2
|
A:HIS87
|
3.2
|
37.0
|
1.0
|
|
CE1
|
A:HIS87
|
3.2
|
39.0
|
1.0
|
|
CE1
|
A:HIS66
|
3.4
|
22.1
|
1.0
|
|
CHA
|
A:HEM1301
|
3.4
|
21.4
|
1.0
|
|
CHD
|
A:HEM1301
|
3.4
|
29.9
|
1.0
|
|
CHB
|
A:HEM1301
|
3.4
|
24.1
|
1.0
|
|
CHC
|
A:HEM1301
|
3.4
|
26.7
|
1.0
|
|
CG
|
A:HIS66
|
4.3
|
22.5
|
1.0
|
|
C2D
|
A:HEM1301
|
4.3
|
27.6
|
1.0
|
|
C3D
|
A:HEM1301
|
4.3
|
24.9
|
1.0
|
|
C2A
|
A:HEM1301
|
4.3
|
31.8
|
1.0
|
|
C3A
|
A:HEM1301
|
4.3
|
32.8
|
1.0
|
|
C2B
|
A:HEM1301
|
4.3
|
30.5
|
1.0
|
|
C3B
|
A:HEM1301
|
4.3
|
24.8
|
1.0
|
|
C3C
|
A:HEM1301
|
4.3
|
32.2
|
1.0
|
|
C2C
|
A:HEM1301
|
4.3
|
28.3
|
1.0
|
|
ND1
|
A:HIS87
|
4.3
|
37.0
|
1.0
|
|
CG
|
A:HIS87
|
4.4
|
36.7
|
1.0
|
|
ND1
|
A:HIS66
|
4.4
|
23.9
|
1.0
|
|
Iron binding site 2 out
of 16 in 2e84
Go back to
Iron Binding Sites List in 2e84
Iron binding site 2 out
of 16 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
 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 High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1302
b:22.9
occ:1.00
|
FE
|
A:HEM1302
|
0.0
|
22.9
|
1.0
|
|
ND
|
A:HEM1302
|
2.0
|
29.7
|
1.0
|
|
NB
|
A:HEM1302
|
2.0
|
26.9
|
1.0
|
|
NC
|
A:HEM1302
|
2.0
|
25.6
|
1.0
|
|
NA
|
A:HEM1302
|
2.0
|
25.6
|
1.0
|
|
NE2
|
A:HIS69
|
2.1
|
23.4
|
1.0
|
|
NE2
|
A:HIS122
|
2.1
|
21.4
|
1.0
|
|
CE1
|
A:HIS122
|
2.9
|
25.9
|
1.0
|
|
CD2
|
A:HIS69
|
3.0
|
15.7
|
1.0
|
|
C1B
|
A:HEM1302
|
3.0
|
30.0
|
1.0
|
|
C1C
|
A:HEM1302
|
3.0
|
22.9
|
1.0
|
|
C4D
|
A:HEM1302
|
3.0
|
30.9
|
1.0
|
|
C1D
|
A:HEM1302
|
3.0
|
27.1
|
1.0
|
|
C4B
|
A:HEM1302
|
3.1
|
26.5
|
1.0
|
|
C1A
|
A:HEM1302
|
3.1
|
31.3
|
1.0
|
|
C4C
|
A:HEM1302
|
3.1
|
28.1
|
1.0
|
|
C4A
|
A:HEM1302
|
3.1
|
28.9
|
1.0
|
|
CE1
|
A:HIS69
|
3.2
|
27.0
|
1.0
|
|
CD2
|
A:HIS122
|
3.3
|
27.1
|
1.0
|
|
CHD
|
A:HEM1302
|
3.4
|
28.5
|
1.0
|
|
CHB
|
A:HEM1302
|
3.4
|
31.2
|
1.0
|
|
CHA
|
A:HEM1302
|
3.4
|
29.4
|
1.0
|
|
CHC
|
A:HEM1302
|
3.4
|
24.2
|
1.0
|
|
ND1
|
A:HIS122
|
4.1
|
26.5
|
1.0
|
|
CG
|
A:HIS69
|
4.2
|
26.3
|
1.0
|
|
ND1
|
A:HIS69
|
4.3
|
32.1
|
1.0
|
|
C3B
|
A:HEM1302
|
4.3
|
24.9
|
1.0
|
|
C2D
|
A:HEM1302
|
4.3
|
26.4
|
1.0
|
|
C2B
|
A:HEM1302
|
4.3
|
25.7
|
1.0
|
|
C3D
|
A:HEM1302
|
4.3
|
30.9
|
1.0
|
|
C2C
|
A:HEM1302
|
4.3
|
24.6
|
1.0
|
|
C3A
|
A:HEM1302
|
4.3
|
33.3
|
1.0
|
|
C3C
|
A:HEM1302
|
4.3
|
25.2
|
1.0
|
|
C2A
|
A:HEM1302
|
4.3
|
32.5
|
1.0
|
|
CG
|
A:HIS122
|
4.3
|
20.1
|
1.0
|
|
CA
|
A:GLY133
|
4.5
|
32.0
|
1.0
|
|
CE1
|
A:PHE64
|
4.6
|
25.8
|
1.0
|
|
N
|
A:GLY133
|
4.7
|
31.5
|
1.0
|
|
Iron binding site 3 out
of 16 in 2e84
Go back to
Iron Binding Sites List in 2e84
Iron binding site 3 out
of 16 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
 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 High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1303
b:42.5
occ:1.00
|
FE
|
A:HEM1303
|
0.0
|
42.5
|
1.0
|
|
ND
|
A:HEM1303
|
2.0
|
46.8
|
1.0
|
|
NC
|
A:HEM1303
|
2.0
|
46.3
|
1.0
|
|
NB
|
A:HEM1303
|
2.0
|
52.5
|
1.0
|
|
NA
|
A:HEM1303
|
2.0
|
49.9
|
1.0
|
|
NE2
|
A:HIS115
|
2.2
|
48.0
|
1.0
|
|
NE2
|
A:HIS143
|
2.4
|
40.8
|
1.0
|
|
C4D
|
A:HEM1303
|
3.0
|
47.7
|
1.0
|
|
C1C
|
A:HEM1303
|
3.0
|
45.0
|
1.0
|
|
C1D
|
A:HEM1303
|
3.0
|
41.5
|
1.0
|
|
C1B
|
A:HEM1303
|
3.0
|
54.5
|
1.0
|
|
C1A
|
A:HEM1303
|
3.1
|
50.0
|
1.0
|
|
C4C
|
A:HEM1303
|
3.1
|
41.2
|
1.0
|
|
C4A
|
A:HEM1303
|
3.1
|
49.9
|
1.0
|
|
C4B
|
A:HEM1303
|
3.1
|
52.0
|
1.0
|
|
CD2
|
A:HIS115
|
3.1
|
49.9
|
1.0
|
|
CD2
|
A:HIS143
|
3.2
|
43.3
|
1.0
|
|
CE1
|
A:HIS115
|
3.2
|
55.5
|
1.0
|
|
CHD
|
A:HEM1303
|
3.4
|
40.5
|
1.0
|
|
CHA
|
A:HEM1303
|
3.4
|
50.6
|
1.0
|
|
CHB
|
A:HEM1303
|
3.4
|
51.0
|
1.0
|
|
CHC
|
A:HEM1303
|
3.4
|
50.2
|
1.0
|
|
CE1
|
A:HIS143
|
3.5
|
45.4
|
1.0
|
|
ND1
|
A:HIS115
|
4.3
|
54.6
|
1.0
|
|
CG
|
A:HIS115
|
4.3
|
48.3
|
1.0
|
|
C2D
|
A:HEM1303
|
4.3
|
39.5
|
1.0
|
|
C3D
|
A:HEM1303
|
4.3
|
43.0
|
1.0
|
|
C2B
|
A:HEM1303
|
4.3
|
56.5
|
1.0
|
|
C3B
|
A:HEM1303
|
4.3
|
54.1
|
1.0
|
|
C3A
|
A:HEM1303
|
4.3
|
55.2
|
1.0
|
|
C2C
|
A:HEM1303
|
4.3
|
42.4
|
1.0
|
|
C2A
|
A:HEM1303
|
4.3
|
54.1
|
1.0
|
|
C3C
|
A:HEM1303
|
4.3
|
41.7
|
1.0
|
|
CG
|
A:HIS143
|
4.4
|
47.8
|
1.0
|
|
ND1
|
A:HIS143
|
4.5
|
46.6
|
1.0
|
|
Iron binding site 4 out
of 16 in 2e84
Go back to
Iron Binding Sites List in 2e84
Iron binding site 4 out
of 16 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
 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 High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1304
b:24.7
occ:1.00
|
FE
|
A:HEM1304
|
0.0
|
24.7
|
1.0
|
|
ND
|
A:HEM1304
|
2.0
|
29.6
|
1.0
|
|
NC
|
A:HEM1304
|
2.0
|
23.5
|
1.0
|
|
NB
|
A:HEM1304
|
2.0
|
28.7
|
1.0
|
|
NA
|
A:HEM1304
|
2.0
|
21.0
|
1.0
|
|
NE2
|
A:HIS162
|
2.2
|
25.9
|
1.0
|
|
NE2
|
A:HIS185
|
2.2
|
18.7
|
1.0
|
|
CD2
|
A:HIS185
|
3.0
|
19.4
|
1.0
|
|
CE1
|
A:HIS162
|
3.0
|
31.6
|
1.0
|
|
C1A
|
A:HEM1304
|
3.0
|
24.9
|
1.0
|
|
C4D
|
A:HEM1304
|
3.0
|
27.9
|
1.0
|
|
C1D
|
A:HEM1304
|
3.0
|
30.6
|
1.0
|
|
C1C
|
A:HEM1304
|
3.0
|
26.1
|
1.0
|
|
C1B
|
A:HEM1304
|
3.0
|
24.2
|
1.0
|
|
C4A
|
A:HEM1304
|
3.1
|
30.2
|
1.0
|
|
C4B
|
A:HEM1304
|
3.1
|
28.6
|
1.0
|
|
C4C
|
A:HEM1304
|
3.1
|
23.3
|
1.0
|
|
CD2
|
A:HIS162
|
3.3
|
26.0
|
1.0
|
|
CE1
|
A:HIS185
|
3.3
|
20.7
|
1.0
|
|
CHA
|
A:HEM1304
|
3.4
|
27.4
|
1.0
|
|
CHD
|
A:HEM1304
|
3.4
|
28.8
|
1.0
|
|
CHB
|
A:HEM1304
|
3.4
|
23.3
|
1.0
|
|
CHC
|
A:HEM1304
|
3.4
|
24.1
|
1.0
|
|
ND1
|
A:HIS162
|
4.2
|
29.2
|
1.0
|
|
CG
|
A:HIS185
|
4.2
|
23.5
|
1.0
|
|
C2D
|
A:HEM1304
|
4.3
|
31.8
|
1.0
|
|
C3D
|
A:HEM1304
|
4.3
|
27.5
|
1.0
|
|
C2A
|
A:HEM1304
|
4.3
|
28.4
|
1.0
|
|
C3A
|
A:HEM1304
|
4.3
|
31.7
|
1.0
|
|
C2B
|
A:HEM1304
|
4.3
|
24.4
|
1.0
|
|
C3B
|
A:HEM1304
|
4.3
|
28.9
|
1.0
|
|
C3C
|
A:HEM1304
|
4.3
|
25.6
|
1.0
|
|
C2C
|
A:HEM1304
|
4.3
|
27.4
|
1.0
|
|
ND1
|
A:HIS185
|
4.3
|
25.4
|
1.0
|
|
CG
|
A:HIS162
|
4.4
|
28.8
|
1.0
|
|
Iron binding site 5 out
of 16 in 2e84
Go back to
Iron Binding Sites List in 2e84
Iron binding site 5 out
of 16 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1305
b:29.1
occ:1.00
|
FE
|
A:HEM1305
|
0.0
|
29.1
|
1.0
|
|
ND
|
A:HEM1305
|
2.0
|
36.0
|
1.0
|
|
NC
|
A:HEM1305
|
2.0
|
34.9
|
1.0
|
|
NB
|
A:HEM1305
|
2.0
|
36.6
|
1.0
|
|
NA
|
A:HEM1305
|
2.0
|
40.4
|
1.0
|
|
NE2
|
A:HIS209
|
2.1
|
16.5
|
1.0
|
|
NE2
|
A:HIS186
|
2.3
|
14.4
|
1.0
|
|
C1C
|
A:HEM1305
|
3.0
|
34.4
|
1.0
|
|
C1D
|
A:HEM1305
|
3.0
|
39.3
|
1.0
|
|
C4D
|
A:HEM1305
|
3.0
|
37.1
|
1.0
|
|
CE1
|
A:HIS209
|
3.1
|
25.8
|
1.0
|
|
C4C
|
A:HEM1305
|
3.1
|
36.8
|
1.0
|
|
C1B
|
A:HEM1305
|
3.1
|
35.1
|
1.0
|
|
C1A
|
A:HEM1305
|
3.1
|
41.2
|
1.0
|
|
C4B
|
A:HEM1305
|
3.1
|
33.2
|
1.0
|
|
C4A
|
A:HEM1305
|
3.1
|
37.8
|
1.0
|
|
CD2
|
A:HIS209
|
3.2
|
25.8
|
1.0
|
|
CE1
|
A:HIS186
|
3.2
|
22.4
|
1.0
|
|
CD2
|
A:HIS186
|
3.3
|
26.1
|
1.0
|
|
CHD
|
A:HEM1305
|
3.4
|
40.3
|
1.0
|
|
CHA
|
A:HEM1305
|
3.4
|
37.7
|
1.0
|
|
CHC
|
A:HEM1305
|
3.4
|
36.7
|
1.0
|
|
CHB
|
A:HEM1305
|
3.4
|
35.5
|
1.0
|
|
ND1
|
A:HIS209
|
4.2
|
25.4
|
1.0
|
|
C2D
|
A:HEM1305
|
4.3
|
40.1
|
1.0
|
|
C3D
|
A:HEM1305
|
4.3
|
40.9
|
1.0
|
|
C3B
|
A:HEM1305
|
4.3
|
31.3
|
1.0
|
|
C2C
|
A:HEM1305
|
4.3
|
33.0
|
1.0
|
|
C2B
|
A:HEM1305
|
4.3
|
34.5
|
1.0
|
|
C3C
|
A:HEM1305
|
4.3
|
35.3
|
1.0
|
|
C2A
|
A:HEM1305
|
4.3
|
40.5
|
1.0
|
|
CG
|
A:HIS209
|
4.3
|
28.9
|
1.0
|
|
C3A
|
A:HEM1305
|
4.3
|
37.1
|
1.0
|
|
ND1
|
A:HIS186
|
4.3
|
24.4
|
1.0
|
|
CG
|
A:HIS186
|
4.4
|
20.8
|
1.0
|
|
CD2
|
A:LEU195
|
4.8
|
39.2
|
1.0
|
|
Iron binding site 6 out
of 16 in 2e84
Go back to
Iron Binding Sites List in 2e84
Iron binding site 6 out
of 16 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1306
b:31.1
occ:1.00
|
FE
|
A:HEM1306
|
0.0
|
31.1
|
1.0
|
|
ND
|
A:HEM1306
|
2.0
|
35.6
|
1.0
|
|
NC
|
A:HEM1306
|
2.0
|
28.1
|
1.0
|
|
NB
|
A:HEM1306
|
2.0
|
30.8
|
1.0
|
|
NA
|
A:HEM1306
|
2.0
|
36.4
|
1.0
|
|
NE2
|
A:HIS232
|
2.2
|
33.0
|
1.0
|
|
NE2
|
A:HIS165
|
2.3
|
33.1
|
1.0
|
|
C4D
|
A:HEM1306
|
3.0
|
36.0
|
1.0
|
|
C1D
|
A:HEM1306
|
3.0
|
37.3
|
1.0
|
|
CD2
|
A:HIS165
|
3.0
|
30.3
|
1.0
|
|
C1C
|
A:HEM1306
|
3.0
|
29.6
|
1.0
|
|
C1A
|
A:HEM1306
|
3.0
|
36.1
|
1.0
|
|
C1B
|
A:HEM1306
|
3.1
|
27.6
|
1.0
|
|
C4C
|
A:HEM1306
|
3.1
|
29.8
|
1.0
|
|
C4B
|
A:HEM1306
|
3.1
|
30.8
|
1.0
|
|
C4A
|
A:HEM1306
|
3.1
|
35.0
|
1.0
|
|
CD2
|
A:HIS232
|
3.1
|
33.1
|
1.0
|
|
CE1
|
A:HIS232
|
3.3
|
35.6
|
1.0
|
|
CHA
|
A:HEM1306
|
3.4
|
36.5
|
1.0
|
|
CHD
|
A:HEM1306
|
3.4
|
34.7
|
1.0
|
|
CHB
|
A:HEM1306
|
3.4
|
32.5
|
1.0
|
|
CHC
|
A:HEM1306
|
3.4
|
27.7
|
1.0
|
|
CE1
|
A:HIS165
|
3.4
|
36.9
|
1.0
|
|
C2D
|
A:HEM1306
|
4.3
|
35.8
|
1.0
|
|
C3D
|
A:HEM1306
|
4.3
|
37.4
|
1.0
|
|
CG
|
A:HIS165
|
4.3
|
34.1
|
1.0
|
|
C3B
|
A:HEM1306
|
4.3
|
28.6
|
1.0
|
|
C2A
|
A:HEM1306
|
4.3
|
35.8
|
1.0
|
|
C2B
|
A:HEM1306
|
4.3
|
27.5
|
1.0
|
|
C3A
|
A:HEM1306
|
4.3
|
36.1
|
1.0
|
|
C2C
|
A:HEM1306
|
4.3
|
31.9
|
1.0
|
|
C3C
|
A:HEM1306
|
4.3
|
32.0
|
1.0
|
|
CG
|
A:HIS232
|
4.3
|
33.5
|
1.0
|
|
ND1
|
A:HIS232
|
4.3
|
34.6
|
1.0
|
|
ND1
|
A:HIS165
|
4.4
|
30.4
|
1.0
|
|
CA
|
A:GLY245
|
4.5
|
32.5
|
1.0
|
|
N
|
A:GLY245
|
4.9
|
33.3
|
1.0
|
|
Iron binding site 7 out
of 16 in 2e84
Go back to
Iron Binding Sites List in 2e84
Iron binding site 7 out
of 16 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1307
b:24.6
occ:1.00
|
FE
|
A:HEM1307
|
0.0
|
24.6
|
1.0
|
|
ND
|
A:HEM1307
|
2.0
|
25.8
|
1.0
|
|
NB
|
A:HEM1307
|
2.0
|
23.2
|
1.0
|
|
NC
|
A:HEM1307
|
2.0
|
28.1
|
1.0
|
|
NA
|
A:HEM1307
|
2.0
|
27.2
|
1.0
|
|
NE2
|
A:HIS253
|
2.2
|
18.1
|
1.0
|
|
NE2
|
A:HIS225
|
2.2
|
22.2
|
1.0
|
|
C4D
|
A:HEM1307
|
3.0
|
25.6
|
1.0
|
|
C1B
|
A:HEM1307
|
3.0
|
25.4
|
1.0
|
|
C4B
|
A:HEM1307
|
3.0
|
23.2
|
1.0
|
|
C1C
|
A:HEM1307
|
3.0
|
28.4
|
1.0
|
|
C1D
|
A:HEM1307
|
3.0
|
30.2
|
1.0
|
|
C1A
|
A:HEM1307
|
3.1
|
29.1
|
1.0
|
|
C4A
|
A:HEM1307
|
3.1
|
34.2
|
1.0
|
|
C4C
|
A:HEM1307
|
3.1
|
30.7
|
1.0
|
|
CD2
|
A:HIS253
|
3.1
|
23.1
|
1.0
|
|
CD2
|
A:HIS225
|
3.1
|
23.4
|
1.0
|
|
CE1
|
A:HIS253
|
3.3
|
25.3
|
1.0
|
|
CE1
|
A:HIS225
|
3.3
|
24.0
|
1.0
|
|
CHA
|
A:HEM1307
|
3.4
|
29.0
|
1.0
|
|
CHC
|
A:HEM1307
|
3.4
|
27.7
|
1.0
|
|
CHB
|
A:HEM1307
|
3.4
|
32.0
|
1.0
|
|
CHD
|
A:HEM1307
|
3.4
|
30.5
|
1.0
|
|
C3B
|
A:HEM1307
|
4.2
|
23.7
|
1.0
|
|
C3D
|
A:HEM1307
|
4.3
|
30.7
|
1.0
|
|
C2B
|
A:HEM1307
|
4.3
|
21.8
|
1.0
|
|
C2D
|
A:HEM1307
|
4.3
|
29.4
|
1.0
|
|
CG
|
A:HIS253
|
4.3
|
27.0
|
1.0
|
|
CG
|
A:HIS225
|
4.3
|
25.6
|
1.0
|
|
C3A
|
A:HEM1307
|
4.3
|
39.0
|
1.0
|
|
C2A
|
A:HEM1307
|
4.3
|
36.0
|
1.0
|
|
C2C
|
A:HEM1307
|
4.3
|
27.8
|
1.0
|
|
ND1
|
A:HIS253
|
4.3
|
21.9
|
1.0
|
|
C3C
|
A:HEM1307
|
4.3
|
33.6
|
1.0
|
|
ND1
|
A:HIS225
|
4.4
|
27.5
|
1.0
|
|
NE1
|
A:TRP152
|
4.9
|
31.0
|
1.0
|
|
Iron binding site 8 out
of 16 in 2e84
Go back to
Iron Binding Sites List in 2e84
Iron binding site 8 out
of 16 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1308
b:21.0
occ:1.00
|
FE
|
A:HEM1308
|
0.0
|
21.0
|
1.0
|
|
ND
|
A:HEM1308
|
2.0
|
20.9
|
1.0
|
|
NB
|
A:HEM1308
|
2.0
|
16.0
|
1.0
|
|
NC
|
A:HEM1308
|
2.0
|
20.9
|
1.0
|
|
NA
|
A:HEM1308
|
2.0
|
19.8
|
1.0
|
|
NE2
|
A:HIS320
|
2.1
|
33.4
|
1.0
|
|
NE2
|
A:HIS306
|
2.2
|
24.7
|
1.0
|
|
CE1
|
A:HIS320
|
3.0
|
29.5
|
1.0
|
|
C4D
|
A:HEM1308
|
3.0
|
26.4
|
1.0
|
|
C1D
|
A:HEM1308
|
3.0
|
23.9
|
1.0
|
|
C1B
|
A:HEM1308
|
3.0
|
19.8
|
1.0
|
|
CD2
|
A:HIS306
|
3.0
|
23.2
|
1.0
|
|
C1C
|
A:HEM1308
|
3.1
|
16.9
|
1.0
|
|
C4B
|
A:HEM1308
|
3.1
|
17.8
|
1.0
|
|
C1A
|
A:HEM1308
|
3.1
|
21.9
|
1.0
|
|
C4A
|
A:HEM1308
|
3.1
|
19.2
|
1.0
|
|
C4C
|
A:HEM1308
|
3.1
|
18.2
|
1.0
|
|
CD2
|
A:HIS320
|
3.2
|
33.7
|
1.0
|
|
CE1
|
A:HIS306
|
3.3
|
33.6
|
1.0
|
|
CHB
|
A:HEM1308
|
3.4
|
21.6
|
1.0
|
|
CHA
|
A:HEM1308
|
3.4
|
21.3
|
1.0
|
|
CHD
|
A:HEM1308
|
3.4
|
21.5
|
1.0
|
|
CHC
|
A:HEM1308
|
3.4
|
20.6
|
1.0
|
|
ND1
|
A:HIS320
|
4.1
|
35.8
|
1.0
|
|
C2D
|
A:HEM1308
|
4.3
|
25.1
|
1.0
|
|
C3D
|
A:HEM1308
|
4.3
|
28.1
|
1.0
|
|
CG
|
A:HIS306
|
4.3
|
26.0
|
1.0
|
|
C2B
|
A:HEM1308
|
4.3
|
18.3
|
1.0
|
|
C3B
|
A:HEM1308
|
4.3
|
16.9
|
1.0
|
|
CG
|
A:HIS320
|
4.3
|
33.3
|
1.0
|
|
C3A
|
A:HEM1308
|
4.3
|
21.6
|
1.0
|
|
C2A
|
A:HEM1308
|
4.3
|
23.7
|
1.0
|
|
C2C
|
A:HEM1308
|
4.3
|
15.3
|
1.0
|
|
C3C
|
A:HEM1308
|
4.3
|
19.0
|
1.0
|
|
ND1
|
A:HIS306
|
4.4
|
25.4
|
1.0
|
|
Iron binding site 9 out
of 16 in 2e84
Go back to
Iron Binding Sites List in 2e84
Iron binding site 9 out
of 16 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1309
b:23.5
occ:1.00
|
FE
|
A:HEM1309
|
0.0
|
23.5
|
1.0
|
|
ND
|
A:HEM1309
|
2.0
|
29.8
|
1.0
|
|
NC
|
A:HEM1309
|
2.0
|
24.7
|
1.0
|
|
NB
|
A:HEM1309
|
2.0
|
27.1
|
1.0
|
|
NA
|
A:HEM1309
|
2.1
|
27.8
|
1.0
|
|
NE2
|
A:HIS331
|
2.2
|
21.8
|
1.0
|
|
NE2
|
A:HIS321
|
2.2
|
25.0
|
1.0
|
|
CE1
|
A:HIS321
|
3.0
|
26.1
|
1.0
|
|
C1D
|
A:HEM1309
|
3.0
|
30.1
|
1.0
|
|
C4D
|
A:HEM1309
|
3.0
|
32.5
|
1.0
|
|
C1C
|
A:HEM1309
|
3.0
|
27.8
|
1.0
|
|
C1B
|
A:HEM1309
|
3.1
|
25.8
|
1.0
|
|
C4C
|
A:HEM1309
|
3.1
|
28.4
|
1.0
|
|
C4B
|
A:HEM1309
|
3.1
|
20.9
|
1.0
|
|
C1A
|
A:HEM1309
|
3.1
|
33.7
|
1.0
|
|
C4A
|
A:HEM1309
|
3.1
|
26.8
|
1.0
|
|
CD2
|
A:HIS331
|
3.1
|
16.5
|
1.0
|
|
CE1
|
A:HIS331
|
3.2
|
15.6
|
1.0
|
|
CHD
|
A:HEM1309
|
3.4
|
28.8
|
1.0
|
|
CHA
|
A:HEM1309
|
3.4
|
33.2
|
1.0
|
|
CD2
|
A:HIS321
|
3.4
|
29.9
|
1.0
|
|
CHB
|
A:HEM1309
|
3.4
|
25.6
|
1.0
|
|
CHC
|
A:HEM1309
|
3.4
|
28.2
|
1.0
|
|
ND1
|
A:HIS321
|
4.2
|
24.3
|
1.0
|
|
C2D
|
A:HEM1309
|
4.3
|
33.7
|
1.0
|
|
C3D
|
A:HEM1309
|
4.3
|
38.7
|
1.0
|
|
CG
|
A:HIS331
|
4.3
|
20.7
|
1.0
|
|
C2B
|
A:HEM1309
|
4.3
|
25.4
|
1.0
|
|
C3B
|
A:HEM1309
|
4.3
|
21.1
|
1.0
|
|
C2C
|
A:HEM1309
|
4.3
|
23.4
|
1.0
|
|
C3C
|
A:HEM1309
|
4.3
|
25.4
|
1.0
|
|
ND1
|
A:HIS331
|
4.3
|
20.4
|
1.0
|
|
C3A
|
A:HEM1309
|
4.3
|
23.9
|
1.0
|
|
C2A
|
A:HEM1309
|
4.3
|
27.6
|
1.0
|
|
CG
|
A:HIS321
|
4.4
|
21.9
|
1.0
|
|
Iron binding site 10 out
of 16 in 2e84
Go back to
Iron Binding Sites List in 2e84
Iron binding site 10 out
of 16 in the Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Crystal Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) in the Presence of Zinc Ion within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1310
b:18.1
occ:1.00
|
FE
|
A:HEM1310
|
0.0
|
18.1
|
1.0
|
|
ND
|
A:HEM1310
|
2.0
|
20.6
|
1.0
|
|
NB
|
A:HEM1310
|
2.0
|
22.4
|
1.0
|
|
NC
|
A:HEM1310
|
2.0
|
23.3
|
1.0
|
|
NA
|
A:HEM1310
|
2.0
|
26.7
|
1.0
|
|
NE2
|
A:HIS309
|
2.1
|
9.1
|
1.0
|
|
NE2
|
A:HIS361
|
2.2
|
16.9
|
1.0
|
|
CD2
|
A:HIS309
|
3.0
|
14.5
|
1.0
|
|
C4D
|
A:HEM1310
|
3.0
|
28.6
|
1.0
|
|
C1D
|
A:HEM1310
|
3.0
|
24.0
|
1.0
|
|
C1A
|
A:HEM1310
|
3.0
|
28.9
|
1.0
|
|
C1B
|
A:HEM1310
|
3.0
|
18.3
|
1.0
|
|
C1C
|
A:HEM1310
|
3.1
|
19.6
|
1.0
|
|
C4B
|
A:HEM1310
|
3.1
|
24.0
|
1.0
|
|
C4A
|
A:HEM1310
|
3.1
|
25.0
|
1.0
|
|
C4C
|
A:HEM1310
|
3.1
|
17.9
|
1.0
|
|
CE1
|
A:HIS361
|
3.2
|
25.8
|
1.0
|
|
CE1
|
A:HIS309
|
3.2
|
17.5
|
1.0
|
|
CD2
|
A:HIS361
|
3.2
|
26.9
|
1.0
|
|
CHA
|
A:HEM1310
|
3.4
|
31.2
|
1.0
|
|
CHD
|
A:HEM1310
|
3.4
|
24.1
|
1.0
|
|
CHB
|
A:HEM1310
|
3.4
|
23.9
|
1.0
|
|
CHC
|
A:HEM1310
|
3.4
|
18.6
|
1.0
|
|
CG
|
A:HIS309
|
4.1
|
14.4
|
1.0
|
|
ND1
|
A:HIS309
|
4.2
|
25.2
|
1.0
|
|
C3D
|
A:HEM1310
|
4.3
|
27.4
|
1.0
|
|
C2D
|
A:HEM1310
|
4.3
|
23.9
|
1.0
|
|
C3B
|
A:HEM1310
|
4.3
|
21.9
|
1.0
|
|
C2B
|
A:HEM1310
|
4.3
|
21.3
|
1.0
|
|
C3A
|
A:HEM1310
|
4.3
|
27.1
|
1.0
|
|
C2A
|
A:HEM1310
|
4.3
|
29.6
|
1.0
|
|
ND1
|
A:HIS361
|
4.3
|
17.9
|
1.0
|
|
C2C
|
A:HEM1310
|
4.3
|
23.9
|
1.0
|
|
C3C
|
A:HEM1310
|
4.3
|
19.3
|
1.0
|
|
CG
|
A:HIS361
|
4.4
|
24.0
|
1.0
|
|
CE1
|
A:PHE304
|
4.8
|
26.1
|
1.0
|
|
Reference:
H.Osuka,
K.Suto,
M.Sato,
N.Shibata,
M.Kitamura,
Y.Morimoto,
K.Ozawa,
H.Akutsu,
Y.Higuchi,
N.Yasuoka.
Structure of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F) To Be Published.
Page generated: Sat Aug 3 21:03:08 2024
|
