Iron in PDB 8gvm: The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days
Enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days
All present enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days:
7.1.1.9;
Protein crystallography data
The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days, PDB code: 8gvm
was solved by
T.Tsukihara,
A.Shimada,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.97 /
1.85
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
183.405,
206.272,
177.609,
90,
90,
90
|
|
R / Rfree (%)
|
16.4 /
18.8
|
Other elements in 8gvm:
The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days
(pdb code 8gvm). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days, PDB code: 8gvm:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8gvm
Go back to
Iron Binding Sites List in 8gvm
Iron binding site 1 out
of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:26.2
occ:1.00
|
FE
|
A:HEA601
|
0.0
|
26.2
|
1.0
|
|
NE2
|
A:HIS61
|
2.0
|
23.9
|
1.0
|
|
NE2
|
A:HIS378
|
2.0
|
26.2
|
1.0
|
|
NB
|
A:HEA601
|
2.0
|
26.5
|
1.0
|
|
NC
|
A:HEA601
|
2.0
|
28.7
|
1.0
|
|
ND
|
A:HEA601
|
2.0
|
24.0
|
1.0
|
|
NA
|
A:HEA601
|
2.0
|
28.6
|
1.0
|
|
CE1
|
A:HIS378
|
2.9
|
31.1
|
1.0
|
|
CE1
|
A:HIS61
|
3.0
|
30.3
|
1.0
|
|
CD2
|
A:HIS61
|
3.0
|
27.5
|
1.0
|
|
C1A
|
A:HEA601
|
3.0
|
28.5
|
1.0
|
|
C4A
|
A:HEA601
|
3.0
|
26.7
|
1.0
|
|
C4C
|
A:HEA601
|
3.0
|
26.7
|
1.0
|
|
C1C
|
A:HEA601
|
3.0
|
28.3
|
1.0
|
|
C1D
|
A:HEA601
|
3.1
|
26.9
|
1.0
|
|
C4D
|
A:HEA601
|
3.1
|
25.3
|
1.0
|
|
C1B
|
A:HEA601
|
3.1
|
24.9
|
1.0
|
|
CD2
|
A:HIS378
|
3.1
|
26.9
|
1.0
|
|
C4B
|
A:HEA601
|
3.1
|
25.2
|
1.0
|
|
CHA
|
A:HEA601
|
3.4
|
24.9
|
1.0
|
|
CHC
|
A:HEA601
|
3.4
|
22.0
|
1.0
|
|
CHB
|
A:HEA601
|
3.5
|
28.6
|
1.0
|
|
CHD
|
A:HEA601
|
3.5
|
24.2
|
1.0
|
|
ND1
|
A:HIS378
|
4.1
|
26.2
|
1.0
|
|
ND1
|
A:HIS61
|
4.1
|
26.8
|
1.0
|
|
CG
|
A:HIS61
|
4.1
|
25.7
|
1.0
|
|
CG
|
A:HIS378
|
4.2
|
24.4
|
1.0
|
|
C3A
|
A:HEA601
|
4.2
|
23.7
|
1.0
|
|
C2A
|
A:HEA601
|
4.2
|
26.9
|
1.0
|
|
C2C
|
A:HEA601
|
4.3
|
24.5
|
1.0
|
|
C3B
|
A:HEA601
|
4.3
|
27.4
|
1.0
|
|
C2D
|
A:HEA601
|
4.3
|
25.7
|
1.0
|
|
C3C
|
A:HEA601
|
4.3
|
24.5
|
1.0
|
|
C2B
|
A:HEA601
|
4.3
|
27.2
|
1.0
|
|
C3D
|
A:HEA601
|
4.3
|
28.9
|
1.0
|
|
OG
|
A:SER382
|
4.7
|
37.8
|
0.5
|
|
Iron binding site 2 out
of 6 in 8gvm
Go back to
Iron Binding Sites List in 8gvm
Iron binding site 2 out
of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:25.9
occ:0.50
|
FE
|
A:HEA602
|
0.0
|
25.9
|
0.5
|
|
FE
|
A:HEA602
|
0.9
|
26.5
|
0.5
|
|
ND
|
A:HEA602
|
1.3
|
22.0
|
0.5
|
|
NC
|
A:HEA602
|
1.8
|
29.4
|
0.5
|
|
NE2
|
A:HIS376
|
2.0
|
29.3
|
1.0
|
|
NB
|
A:HEA602
|
2.0
|
24.9
|
0.5
|
|
ND
|
A:HEA602
|
2.0
|
30.6
|
0.5
|
|
NA
|
A:HEA602
|
2.0
|
26.5
|
0.5
|
|
NC
|
A:HEA602
|
2.0
|
20.4
|
0.5
|
|
N1
|
A:AZI607
|
2.2
|
34.5
|
0.8
|
|
C1D
|
A:HEA602
|
2.3
|
21.6
|
0.5
|
|
C4C
|
A:HEA602
|
2.5
|
34.0
|
0.5
|
|
NA
|
A:HEA602
|
2.5
|
31.3
|
0.5
|
|
C4D
|
A:HEA602
|
2.6
|
20.9
|
0.5
|
|
N1
|
A:AZI607
|
2.6
|
42.5
|
0.1
|
|
CHD
|
A:HEA602
|
2.8
|
19.3
|
0.5
|
|
NB
|
A:HEA602
|
2.8
|
37.1
|
0.5
|
|
CD2
|
A:HIS376
|
3.0
|
29.0
|
1.0
|
|
C4D
|
A:HEA602
|
3.0
|
27.1
|
0.5
|
|
C4B
|
A:HEA602
|
3.0
|
35.6
|
0.5
|
|
N2
|
A:AZI607
|
3.0
|
21.6
|
0.1
|
|
N2
|
A:AZI607
|
3.0
|
30.1
|
0.8
|
|
C1C
|
A:HEA602
|
3.0
|
31.5
|
0.5
|
|
C1A
|
A:HEA602
|
3.0
|
25.9
|
0.5
|
|
CE1
|
A:HIS376
|
3.1
|
30.0
|
1.0
|
|
C1B
|
A:HEA602
|
3.1
|
18.3
|
0.5
|
|
C1C
|
A:HEA602
|
3.1
|
32.7
|
0.5
|
|
C4A
|
A:HEA602
|
3.1
|
20.2
|
0.5
|
|
C1D
|
A:HEA602
|
3.1
|
25.2
|
0.5
|
|
C4C
|
A:HEA602
|
3.1
|
28.4
|
0.5
|
|
C1A
|
A:HEA602
|
3.3
|
33.6
|
0.5
|
|
CHA
|
A:HEA602
|
3.3
|
17.8
|
0.5
|
|
CHC
|
A:HEA602
|
3.4
|
17.0
|
0.5
|
|
CHA
|
A:HEA602
|
3.4
|
32.4
|
0.5
|
|
CHB
|
A:HEA602
|
3.5
|
28.7
|
0.5
|
|
C2D
|
A:HEA602
|
3.5
|
26.2
|
0.5
|
|
CHD
|
A:HEA602
|
3.6
|
23.0
|
0.5
|
|
C4B
|
A:HEA602
|
3.7
|
31.7
|
0.5
|
|
C3D
|
A:HEA602
|
3.7
|
25.1
|
0.5
|
|
C4A
|
A:HEA602
|
3.7
|
33.9
|
0.5
|
|
CHC
|
A:HEA602
|
3.8
|
24.8
|
0.5
|
|
N3
|
A:AZI607
|
3.8
|
29.1
|
0.1
|
|
C3C
|
A:HEA602
|
3.8
|
21.9
|
0.5
|
|
C1B
|
A:HEA602
|
3.9
|
32.0
|
0.5
|
|
C2C
|
A:HEA602
|
4.1
|
26.8
|
0.5
|
|
CG
|
A:HIS376
|
4.1
|
32.1
|
1.0
|
|
ND1
|
A:HIS376
|
4.2
|
28.5
|
1.0
|
|
N3
|
A:AZI607
|
4.2
|
32.0
|
0.8
|
|
N1
|
A:AZI606
|
4.2
|
27.5
|
0.8
|
|
C3D
|
A:HEA602
|
4.2
|
27.9
|
0.5
|
|
C3B
|
A:HEA602
|
4.2
|
22.8
|
0.5
|
|
CHB
|
A:HEA602
|
4.2
|
22.7
|
0.5
|
|
C2B
|
A:HEA602
|
4.2
|
35.9
|
0.5
|
|
C3A
|
A:HEA602
|
4.2
|
34.8
|
0.5
|
|
C2A
|
A:HEA602
|
4.2
|
26.8
|
0.5
|
|
C2D
|
A:HEA602
|
4.3
|
22.2
|
0.5
|
|
C3C
|
A:HEA602
|
4.3
|
27.6
|
0.5
|
|
C2C
|
A:HEA602
|
4.3
|
34.8
|
0.5
|
|
CG1
|
A:VAL380
|
4.6
|
20.1
|
0.5
|
|
C2A
|
A:HEA602
|
4.6
|
20.7
|
0.5
|
|
N2
|
A:AZI606
|
4.7
|
30.8
|
0.8
|
|
C3A
|
A:HEA602
|
4.8
|
18.1
|
0.5
|
|
CMD
|
A:HEA602
|
4.9
|
19.8
|
0.5
|
|
CU
|
A:CU603
|
5.0
|
28.7
|
1.0
|
|
C3B
|
A:HEA602
|
5.0
|
27.7
|
0.5
|
|
Iron binding site 3 out
of 6 in 8gvm
Go back to
Iron Binding Sites List in 8gvm
Iron binding site 3 out
of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:26.5
occ:0.50
|
FE
|
A:HEA602
|
0.0
|
26.5
|
0.5
|
|
FE
|
A:HEA602
|
0.9
|
25.9
|
0.5
|
|
NB
|
A:HEA602
|
1.3
|
24.9
|
0.5
|
|
NA
|
A:HEA602
|
1.7
|
26.5
|
0.5
|
|
NA
|
A:HEA602
|
2.0
|
31.3
|
0.5
|
|
NB
|
A:HEA602
|
2.0
|
37.1
|
0.5
|
|
NC
|
A:HEA602
|
2.0
|
29.4
|
0.5
|
|
ND
|
A:HEA602
|
2.0
|
22.0
|
0.5
|
|
NE2
|
A:HIS376
|
2.1
|
29.3
|
1.0
|
|
N1
|
A:AZI607
|
2.1
|
34.5
|
0.8
|
|
C1B
|
A:HEA602
|
2.2
|
18.3
|
0.5
|
|
C4A
|
A:HEA602
|
2.4
|
20.2
|
0.5
|
|
N1
|
A:AZI607
|
2.5
|
42.5
|
0.1
|
|
N2
|
A:AZI607
|
2.6
|
30.1
|
0.8
|
|
C4B
|
A:HEA602
|
2.6
|
35.6
|
0.5
|
|
NC
|
A:HEA602
|
2.6
|
20.4
|
0.5
|
|
CHB
|
A:HEA602
|
2.7
|
28.7
|
0.5
|
|
ND
|
A:HEA602
|
2.8
|
30.6
|
0.5
|
|
C1A
|
A:HEA602
|
3.0
|
25.9
|
0.5
|
|
C4A
|
A:HEA602
|
3.0
|
33.9
|
0.5
|
|
CE1
|
A:HIS376
|
3.0
|
30.0
|
1.0
|
|
C1B
|
A:HEA602
|
3.0
|
32.0
|
0.5
|
|
C1C
|
A:HEA602
|
3.0
|
31.5
|
0.5
|
|
C1A
|
A:HEA602
|
3.0
|
33.6
|
0.5
|
|
C4B
|
A:HEA602
|
3.0
|
31.7
|
0.5
|
|
C4D
|
A:HEA602
|
3.0
|
20.9
|
0.5
|
|
C4C
|
A:HEA602
|
3.1
|
34.0
|
0.5
|
|
C1D
|
A:HEA602
|
3.1
|
21.6
|
0.5
|
|
CD2
|
A:HIS376
|
3.1
|
29.0
|
1.0
|
|
N2
|
A:AZI607
|
3.2
|
21.6
|
0.1
|
|
CHC
|
A:HEA602
|
3.3
|
17.0
|
0.5
|
|
CHB
|
A:HEA602
|
3.4
|
22.7
|
0.5
|
|
C1C
|
A:HEA602
|
3.4
|
32.7
|
0.5
|
|
CHC
|
A:HEA602
|
3.4
|
24.8
|
0.5
|
|
CHA
|
A:HEA602
|
3.4
|
17.8
|
0.5
|
|
C2B
|
A:HEA602
|
3.5
|
35.9
|
0.5
|
|
N3
|
A:AZI607
|
3.6
|
32.0
|
0.8
|
|
CHD
|
A:HEA602
|
3.6
|
19.3
|
0.5
|
|
C4D
|
A:HEA602
|
3.6
|
27.1
|
0.5
|
|
C3B
|
A:HEA602
|
3.6
|
22.8
|
0.5
|
|
C3A
|
A:HEA602
|
3.7
|
34.8
|
0.5
|
|
CHA
|
A:HEA602
|
3.7
|
32.4
|
0.5
|
|
C4C
|
A:HEA602
|
3.8
|
28.4
|
0.5
|
|
C1D
|
A:HEA602
|
3.9
|
25.2
|
0.5
|
|
C2A
|
A:HEA602
|
4.0
|
26.8
|
0.5
|
|
ND1
|
A:HIS376
|
4.2
|
28.5
|
1.0
|
|
C3A
|
A:HEA602
|
4.2
|
18.1
|
0.5
|
|
N3
|
A:AZI607
|
4.2
|
29.1
|
0.1
|
|
C2A
|
A:HEA602
|
4.2
|
20.7
|
0.5
|
|
C2B
|
A:HEA602
|
4.2
|
32.8
|
0.5
|
|
CG
|
A:HIS376
|
4.2
|
32.1
|
1.0
|
|
C3B
|
A:HEA602
|
4.3
|
27.7
|
0.5
|
|
C2C
|
A:HEA602
|
4.3
|
26.8
|
0.5
|
|
C3C
|
A:HEA602
|
4.3
|
21.9
|
0.5
|
|
C3D
|
A:HEA602
|
4.3
|
25.1
|
0.5
|
|
C2D
|
A:HEA602
|
4.3
|
26.2
|
0.5
|
|
CHD
|
A:HEA602
|
4.4
|
23.0
|
0.5
|
|
N1
|
A:AZI606
|
4.5
|
27.5
|
0.8
|
|
C2C
|
A:HEA602
|
4.7
|
34.8
|
0.5
|
|
CA
|
A:GLY355
|
4.8
|
28.1
|
1.0
|
|
CMB
|
A:HEA602
|
4.8
|
29.7
|
0.5
|
|
C3D
|
A:HEA602
|
4.9
|
27.9
|
0.5
|
|
C3C
|
A:HEA602
|
4.9
|
27.6
|
0.5
|
|
CU
|
A:CU603
|
4.9
|
28.7
|
1.0
|
|
CMA
|
A:HEA602
|
5.0
|
51.5
|
0.5
|
|
Iron binding site 4 out
of 6 in 8gvm
Go back to
Iron Binding Sites List in 8gvm
Iron binding site 4 out
of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe602
b:32.2
occ:1.00
|
FE
|
N:HEA602
|
0.0
|
32.2
|
1.0
|
|
NE2
|
N:HIS61
|
2.0
|
29.5
|
1.0
|
|
NC
|
N:HEA602
|
2.0
|
31.7
|
1.0
|
|
NE2
|
N:HIS378
|
2.0
|
34.6
|
1.0
|
|
NA
|
N:HEA602
|
2.0
|
35.7
|
1.0
|
|
ND
|
N:HEA602
|
2.0
|
30.1
|
1.0
|
|
NB
|
N:HEA602
|
2.0
|
32.9
|
1.0
|
|
CE1
|
N:HIS378
|
2.9
|
35.8
|
1.0
|
|
CE1
|
N:HIS61
|
3.0
|
35.9
|
1.0
|
|
CD2
|
N:HIS61
|
3.0
|
31.8
|
1.0
|
|
C1A
|
N:HEA602
|
3.0
|
32.8
|
1.0
|
|
C1D
|
N:HEA602
|
3.0
|
31.3
|
1.0
|
|
C4A
|
N:HEA602
|
3.0
|
33.2
|
1.0
|
|
C4C
|
N:HEA602
|
3.0
|
38.2
|
1.0
|
|
C1B
|
N:HEA602
|
3.0
|
32.4
|
1.0
|
|
C1C
|
N:HEA602
|
3.0
|
35.4
|
1.0
|
|
C4B
|
N:HEA602
|
3.1
|
34.0
|
1.0
|
|
CD2
|
N:HIS378
|
3.1
|
31.2
|
1.0
|
|
C4D
|
N:HEA602
|
3.1
|
31.7
|
1.0
|
|
CHB
|
N:HEA602
|
3.4
|
31.8
|
1.0
|
|
CHD
|
N:HEA602
|
3.4
|
29.8
|
1.0
|
|
CHA
|
N:HEA602
|
3.5
|
32.8
|
1.0
|
|
CHC
|
N:HEA602
|
3.5
|
29.8
|
1.0
|
|
ND1
|
N:HIS378
|
4.1
|
34.8
|
1.0
|
|
ND1
|
N:HIS61
|
4.1
|
30.8
|
1.0
|
|
CG
|
N:HIS61
|
4.1
|
33.7
|
1.0
|
|
CG
|
N:HIS378
|
4.2
|
35.4
|
1.0
|
|
C2A
|
N:HEA602
|
4.2
|
32.0
|
1.0
|
|
C3A
|
N:HEA602
|
4.2
|
33.0
|
1.0
|
|
C3C
|
N:HEA602
|
4.2
|
36.1
|
1.0
|
|
C3B
|
N:HEA602
|
4.3
|
34.4
|
1.0
|
|
C2D
|
N:HEA602
|
4.3
|
32.0
|
1.0
|
|
C2C
|
N:HEA602
|
4.3
|
30.2
|
1.0
|
|
C2B
|
N:HEA602
|
4.3
|
35.8
|
1.0
|
|
C3D
|
N:HEA602
|
4.3
|
27.7
|
1.0
|
|
OG
|
N:SER382
|
4.9
|
53.8
|
0.5
|
|
CE1
|
N:PHE377
|
4.9
|
35.4
|
1.0
|
|
Iron binding site 5 out
of 6 in 8gvm
Go back to
Iron Binding Sites List in 8gvm
Iron binding site 5 out
of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe603
b:27.5
occ:0.50
|
FE
|
N:HEA603
|
0.0
|
27.5
|
0.5
|
|
FE
|
N:HEA603
|
1.0
|
30.2
|
0.5
|
|
ND
|
N:HEA603
|
1.5
|
26.3
|
0.5
|
|
NC
|
N:HEA603
|
1.6
|
27.8
|
0.5
|
|
NC
|
N:HEA603
|
2.0
|
25.1
|
0.5
|
|
ND
|
N:HEA603
|
2.0
|
40.1
|
0.5
|
|
NA
|
N:HEA603
|
2.0
|
30.3
|
0.5
|
|
NB
|
N:HEA603
|
2.0
|
21.4
|
0.5
|
|
NE2
|
N:HIS376
|
2.0
|
35.3
|
1.0
|
|
C1D
|
N:HEA603
|
2.2
|
19.4
|
0.5
|
|
N1
|
N:AZI608
|
2.2
|
40.9
|
0.9
|
|
C4C
|
N:HEA603
|
2.2
|
41.5
|
0.5
|
|
CHD
|
N:HEA603
|
2.4
|
19.6
|
0.5
|
|
N3
|
N:AZI608
|
2.5
|
39.1
|
0.1
|
|
C4D
|
N:HEA603
|
2.7
|
31.0
|
0.5
|
|
NA
|
N:HEA603
|
2.7
|
32.8
|
0.5
|
|
NB
|
N:HEA603
|
2.9
|
43.5
|
0.5
|
|
C1C
|
N:HEA603
|
2.9
|
37.1
|
0.5
|
|
N2
|
N:AZI608
|
2.9
|
42.4
|
0.9
|
|
C4D
|
N:HEA603
|
3.0
|
26.5
|
0.5
|
|
C1C
|
N:HEA603
|
3.0
|
31.3
|
0.5
|
|
C1A
|
N:HEA603
|
3.0
|
24.0
|
0.5
|
|
CE1
|
N:HIS376
|
3.0
|
33.0
|
1.0
|
|
C1B
|
N:HEA603
|
3.0
|
16.5
|
0.5
|
|
C4B
|
N:HEA603
|
3.0
|
21.8
|
0.5
|
|
C4A
|
N:HEA603
|
3.0
|
29.1
|
0.5
|
|
C4C
|
N:HEA603
|
3.0
|
24.4
|
0.5
|
|
CD2
|
N:HIS376
|
3.1
|
35.0
|
1.0
|
|
N2
|
N:AZI608
|
3.1
|
29.6
|
0.1
|
|
C1D
|
N:HEA603
|
3.1
|
27.1
|
0.5
|
|
CHA
|
N:HEA603
|
3.4
|
23.5
|
0.5
|
|
C1A
|
N:HEA603
|
3.4
|
35.6
|
0.5
|
|
CHC
|
N:HEA603
|
3.4
|
18.6
|
0.5
|
|
CHB
|
N:HEA603
|
3.5
|
27.4
|
0.5
|
|
CHA
|
N:HEA603
|
3.5
|
25.4
|
0.5
|
|
C2D
|
N:HEA603
|
3.5
|
30.5
|
0.5
|
|
CHD
|
N:HEA603
|
3.5
|
23.8
|
0.5
|
|
C3C
|
N:HEA603
|
3.6
|
23.1
|
0.5
|
|
C4B
|
N:HEA603
|
3.7
|
31.2
|
0.5
|
|
C3D
|
N:HEA603
|
3.8
|
31.2
|
0.5
|
|
CHC
|
N:HEA603
|
3.8
|
31.9
|
0.5
|
|
C2C
|
N:HEA603
|
3.9
|
34.7
|
0.5
|
|
C4A
|
N:HEA603
|
3.9
|
36.3
|
0.5
|
|
N3
|
N:AZI608
|
4.0
|
38.7
|
0.9
|
|
N1
|
N:AZI608
|
4.0
|
38.8
|
0.1
|
|
C1B
|
N:HEA603
|
4.0
|
31.8
|
0.5
|
|
N1
|
N:AZI607
|
4.1
|
34.8
|
0.9
|
|
ND1
|
N:HIS376
|
4.2
|
33.4
|
1.0
|
|
CG
|
N:HIS376
|
4.2
|
32.6
|
1.0
|
|
C3D
|
N:HEA603
|
4.2
|
22.2
|
0.5
|
|
C3C
|
N:HEA603
|
4.2
|
35.5
|
0.5
|
|
C2C
|
N:HEA603
|
4.2
|
26.7
|
0.5
|
|
C3A
|
N:HEA603
|
4.2
|
30.1
|
0.5
|
|
C2A
|
N:HEA603
|
4.2
|
32.2
|
0.5
|
|
C3B
|
N:HEA603
|
4.2
|
29.0
|
0.5
|
|
C2B
|
N:HEA603
|
4.3
|
27.6
|
0.5
|
|
C2D
|
N:HEA603
|
4.3
|
23.2
|
0.5
|
|
CHB
|
N:HEA603
|
4.4
|
26.3
|
0.5
|
|
CG1
|
N:VAL380
|
4.6
|
28.8
|
0.5
|
|
CMD
|
N:HEA603
|
4.7
|
33.2
|
0.5
|
|
N2
|
N:AZI607
|
4.7
|
39.4
|
0.9
|
|
C2A
|
N:HEA603
|
4.8
|
28.1
|
0.5
|
|
CAC
|
N:HEA603
|
4.8
|
27.4
|
0.5
|
|
CU
|
N:CU604
|
4.9
|
31.4
|
1.0
|
|
C3A
|
N:HEA603
|
5.0
|
32.6
|
0.5
|
|
Iron binding site 6 out
of 6 in 8gvm
Go back to
Iron Binding Sites List in 8gvm
Iron binding site 6 out
of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe603
b:30.2
occ:0.50
|
FE
|
N:HEA603
|
0.0
|
30.2
|
0.5
|
|
FE
|
N:HEA603
|
1.0
|
27.5
|
0.5
|
|
NB
|
N:HEA603
|
1.4
|
21.4
|
0.5
|
|
NA
|
N:HEA603
|
1.6
|
30.3
|
0.5
|
|
NC
|
N:HEA603
|
2.0
|
27.8
|
0.5
|
|
NA
|
N:HEA603
|
2.0
|
32.8
|
0.5
|
|
NB
|
N:HEA603
|
2.0
|
43.5
|
0.5
|
|
NE2
|
N:HIS376
|
2.1
|
35.3
|
1.0
|
|
ND
|
N:HEA603
|
2.1
|
26.3
|
0.5
|
|
C1B
|
N:HEA603
|
2.1
|
16.5
|
0.5
|
|
C4A
|
N:HEA603
|
2.2
|
29.1
|
0.5
|
|
N1
|
N:AZI608
|
2.2
|
40.9
|
0.9
|
|
CHB
|
N:HEA603
|
2.5
|
27.4
|
0.5
|
|
N3
|
N:AZI608
|
2.5
|
39.1
|
0.1
|
|
N2
|
N:AZI608
|
2.6
|
42.4
|
0.9
|
|
C4B
|
N:HEA603
|
2.7
|
21.8
|
0.5
|
|
NC
|
N:HEA603
|
2.8
|
25.1
|
0.5
|
|
C1A
|
N:HEA603
|
2.9
|
24.0
|
0.5
|
|
ND
|
N:HEA603
|
2.9
|
40.1
|
0.5
|
|
CE1
|
N:HIS376
|
3.0
|
33.0
|
1.0
|
|
C4A
|
N:HEA603
|
3.0
|
36.3
|
0.5
|
|
C1A
|
N:HEA603
|
3.0
|
35.6
|
0.5
|
|
C4C
|
N:HEA603
|
3.0
|
41.5
|
0.5
|
|
C1C
|
N:HEA603
|
3.0
|
37.1
|
0.5
|
|
C1B
|
N:HEA603
|
3.1
|
31.8
|
0.5
|
|
C4B
|
N:HEA603
|
3.1
|
31.2
|
0.5
|
|
C1D
|
N:HEA603
|
3.1
|
19.4
|
0.5
|
|
CD2
|
N:HIS376
|
3.1
|
35.0
|
1.0
|
|
C4D
|
N:HEA603
|
3.1
|
31.0
|
0.5
|
|
CHB
|
N:HEA603
|
3.4
|
26.3
|
0.5
|
|
CHD
|
N:HEA603
|
3.4
|
19.6
|
0.5
|
|
N2
|
N:AZI608
|
3.4
|
29.6
|
0.1
|
|
C2B
|
N:HEA603
|
3.4
|
27.6
|
0.5
|
|
N3
|
N:AZI608
|
3.4
|
38.7
|
0.9
|
|
CHA
|
N:HEA603
|
3.5
|
25.4
|
0.5
|
|
C1C
|
N:HEA603
|
3.5
|
31.3
|
0.5
|
|
CHC
|
N:HEA603
|
3.5
|
31.9
|
0.5
|
|
CHC
|
N:HEA603
|
3.5
|
18.6
|
0.5
|
|
C3A
|
N:HEA603
|
3.5
|
30.1
|
0.5
|
|
C4D
|
N:HEA603
|
3.6
|
26.5
|
0.5
|
|
CHA
|
N:HEA603
|
3.6
|
23.5
|
0.5
|
|
C3B
|
N:HEA603
|
3.7
|
29.0
|
0.5
|
|
C2A
|
N:HEA603
|
3.8
|
32.2
|
0.5
|
|
C4C
|
N:HEA603
|
4.0
|
24.4
|
0.5
|
|
C1D
|
N:HEA603
|
4.1
|
27.1
|
0.5
|
|
ND1
|
N:HIS376
|
4.1
|
33.4
|
1.0
|
|
C3A
|
N:HEA603
|
4.2
|
32.6
|
0.5
|
|
CG
|
N:HIS376
|
4.2
|
32.6
|
1.0
|
|
C2A
|
N:HEA603
|
4.2
|
28.1
|
0.5
|
|
C3C
|
N:HEA603
|
4.2
|
23.1
|
0.5
|
|
C2C
|
N:HEA603
|
4.2
|
34.7
|
0.5
|
|
C2B
|
N:HEA603
|
4.3
|
41.3
|
0.5
|
|
C3B
|
N:HEA603
|
4.3
|
29.9
|
0.5
|
|
C2D
|
N:HEA603
|
4.3
|
30.5
|
0.5
|
|
C3D
|
N:HEA603
|
4.4
|
31.2
|
0.5
|
|
N1
|
N:AZI607
|
4.5
|
34.8
|
0.9
|
|
N1
|
N:AZI608
|
4.5
|
38.8
|
0.1
|
|
CHD
|
N:HEA603
|
4.5
|
23.8
|
0.5
|
|
CA
|
N:GLY355
|
4.7
|
37.2
|
1.0
|
|
CMB
|
N:HEA603
|
4.7
|
25.0
|
0.5
|
|
CMA
|
N:HEA603
|
4.8
|
38.3
|
0.5
|
|
C2C
|
N:HEA603
|
4.8
|
26.7
|
0.5
|
|
C3D
|
N:HEA603
|
4.9
|
22.2
|
0.5
|
|
CU
|
N:CU604
|
5.0
|
31.4
|
1.0
|
|
Reference:
A.Shimada,
K.Hatano,
H.Tadehara,
N.Yano,
K.Sinzawa-Itoh,
E.Yamashita,
K.Mutamoto,
T.Tsukihara,
S.Yoshikawa.
X-Ray Structural Analyses of Azide-Bound Cytochromecoxidases Reveal That the H-Pathway Is Critically Important For the Proton-Pumping Activity J. Biol. Chem. V. 293 14868 2018.
ISSN: ESSN ESSN 1083-351X
PubMed: 30077971
DOI: 10.1074/JBC.RA118.003123
Page generated: Sat Aug 10 05:00:57 2024
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