Iron in PDB 5w97: Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature
Enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature
All present enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature:
1.9.3.1;
Protein crystallography data
The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97
was solved by
D.L.Rousseau,
S.-R.Yeh,
I.Ishigami,
N.A.Zatsepin,
T.D.Grant,
P.Fromme,
R.Fromme,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.86 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
178.300,
189.000,
209.000,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.8 /
25.2
|
Other elements in 5w97:
The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature
(pdb code 5w97). 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 Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 5w97
Go back to
Iron Binding Sites List in 5w97
Iron binding site 1 out
of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature
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 Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:24.9
occ:1.00
|
FE
|
A:HEA601
|
0.0
|
24.9
|
1.0
|
NE2
|
A:HIS378
|
1.9
|
23.5
|
1.0
|
NE2
|
A:HIS61
|
1.9
|
21.0
|
1.0
|
NA
|
A:HEA601
|
2.0
|
25.4
|
1.0
|
ND
|
A:HEA601
|
2.1
|
23.9
|
1.0
|
NB
|
A:HEA601
|
2.1
|
24.6
|
1.0
|
NC
|
A:HEA601
|
2.1
|
25.3
|
1.0
|
CE1
|
A:HIS378
|
2.8
|
25.5
|
1.0
|
CD2
|
A:HIS61
|
2.9
|
21.6
|
1.0
|
CE1
|
A:HIS61
|
3.0
|
22.1
|
1.0
|
CD2
|
A:HIS378
|
3.0
|
23.4
|
1.0
|
C1A
|
A:HEA601
|
3.1
|
22.9
|
1.0
|
C4A
|
A:HEA601
|
3.1
|
24.9
|
1.0
|
C1D
|
A:HEA601
|
3.1
|
24.7
|
1.0
|
C4B
|
A:HEA601
|
3.1
|
24.1
|
1.0
|
C4D
|
A:HEA601
|
3.1
|
22.7
|
1.0
|
C1C
|
A:HEA601
|
3.1
|
25.0
|
1.0
|
C4C
|
A:HEA601
|
3.1
|
24.3
|
1.0
|
C1B
|
A:HEA601
|
3.1
|
27.5
|
1.0
|
CHC
|
A:HEA601
|
3.4
|
24.1
|
1.0
|
CHD
|
A:HEA601
|
3.4
|
24.5
|
1.0
|
CHA
|
A:HEA601
|
3.5
|
24.2
|
1.0
|
CHB
|
A:HEA601
|
3.5
|
26.2
|
1.0
|
ND1
|
A:HIS378
|
4.0
|
24.2
|
1.0
|
CG
|
A:HIS61
|
4.1
|
21.8
|
1.0
|
ND1
|
A:HIS61
|
4.1
|
21.3
|
1.0
|
CG
|
A:HIS378
|
4.1
|
22.7
|
1.0
|
C3A
|
A:HEA601
|
4.3
|
25.1
|
1.0
|
C2A
|
A:HEA601
|
4.3
|
25.8
|
1.0
|
C3D
|
A:HEA601
|
4.4
|
22.9
|
1.0
|
C3C
|
A:HEA601
|
4.4
|
25.4
|
1.0
|
C2D
|
A:HEA601
|
4.4
|
24.9
|
1.0
|
C3B
|
A:HEA601
|
4.4
|
26.0
|
1.0
|
C2C
|
A:HEA601
|
4.4
|
26.0
|
1.0
|
C2B
|
A:HEA601
|
4.5
|
25.5
|
1.0
|
CE1
|
A:PHE377
|
4.9
|
23.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 5w97
Go back to
Iron Binding Sites List in 5w97
Iron binding site 2 out
of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature
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 Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:23.8
occ:1.00
|
FE
|
A:HEA602
|
0.0
|
23.8
|
1.0
|
C
|
A:CMO609
|
1.9
|
23.5
|
1.0
|
NE2
|
A:HIS376
|
2.0
|
26.6
|
1.0
|
NA
|
A:HEA602
|
2.0
|
21.3
|
1.0
|
ND
|
A:HEA602
|
2.0
|
20.4
|
1.0
|
NB
|
A:HEA602
|
2.1
|
21.7
|
1.0
|
NC
|
A:HEA602
|
2.1
|
23.6
|
1.0
|
CE1
|
A:HIS376
|
2.9
|
26.2
|
1.0
|
O
|
A:CMO609
|
2.9
|
24.4
|
1.0
|
C4D
|
A:HEA602
|
3.0
|
22.3
|
1.0
|
C1A
|
A:HEA602
|
3.0
|
21.4
|
1.0
|
C1D
|
A:HEA602
|
3.1
|
22.0
|
1.0
|
C4A
|
A:HEA602
|
3.1
|
21.0
|
1.0
|
CD2
|
A:HIS376
|
3.1
|
24.7
|
1.0
|
C4B
|
A:HEA602
|
3.1
|
22.2
|
1.0
|
C1C
|
A:HEA602
|
3.1
|
23.2
|
1.0
|
C1B
|
A:HEA602
|
3.1
|
23.1
|
1.0
|
C4C
|
A:HEA602
|
3.1
|
22.7
|
1.0
|
CHC
|
A:HEA602
|
3.4
|
22.2
|
1.0
|
CHA
|
A:HEA602
|
3.4
|
22.5
|
1.0
|
CHD
|
A:HEA602
|
3.5
|
21.5
|
1.0
|
CHB
|
A:HEA602
|
3.5
|
22.6
|
1.0
|
ND1
|
A:HIS376
|
4.1
|
24.0
|
1.0
|
CG
|
A:HIS376
|
4.2
|
24.1
|
1.0
|
C3A
|
A:HEA602
|
4.3
|
21.9
|
1.0
|
C2A
|
A:HEA602
|
4.3
|
23.0
|
1.0
|
C3D
|
A:HEA602
|
4.4
|
22.9
|
1.0
|
C2D
|
A:HEA602
|
4.4
|
22.2
|
1.0
|
C3B
|
A:HEA602
|
4.4
|
22.1
|
1.0
|
C2B
|
A:HEA602
|
4.4
|
21.7
|
1.0
|
C3C
|
A:HEA602
|
4.4
|
22.9
|
1.0
|
C2C
|
A:HEA602
|
4.4
|
23.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 5w97
Go back to
Iron Binding Sites List in 5w97
Iron binding site 3 out
of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature
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 Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe601
b:40.9
occ:1.00
|
FE
|
a:HEA601
|
0.0
|
40.9
|
1.0
|
NE2
|
a:HIS61
|
1.9
|
42.0
|
1.0
|
NE2
|
a:HIS378
|
1.9
|
33.6
|
1.0
|
NA
|
a:HEA601
|
2.0
|
38.3
|
1.0
|
NC
|
a:HEA601
|
2.1
|
39.1
|
1.0
|
ND
|
a:HEA601
|
2.1
|
40.4
|
1.0
|
NB
|
a:HEA601
|
2.1
|
43.5
|
1.0
|
CD2
|
a:HIS61
|
2.8
|
41.0
|
1.0
|
CE1
|
a:HIS378
|
2.9
|
33.2
|
1.0
|
CE1
|
a:HIS61
|
3.0
|
41.3
|
1.0
|
C4A
|
a:HEA601
|
3.0
|
40.2
|
1.0
|
CD2
|
a:HIS378
|
3.0
|
32.0
|
1.0
|
C4C
|
a:HEA601
|
3.1
|
38.7
|
1.0
|
C1A
|
a:HEA601
|
3.1
|
41.8
|
1.0
|
C1C
|
a:HEA601
|
3.1
|
43.1
|
1.0
|
C1D
|
a:HEA601
|
3.1
|
39.7
|
1.0
|
C4B
|
a:HEA601
|
3.1
|
39.5
|
1.0
|
C4D
|
a:HEA601
|
3.1
|
39.3
|
1.0
|
C1B
|
a:HEA601
|
3.1
|
41.6
|
1.0
|
CHD
|
a:HEA601
|
3.4
|
39.5
|
1.0
|
CHC
|
a:HEA601
|
3.5
|
40.6
|
1.0
|
CHB
|
a:HEA601
|
3.5
|
40.0
|
1.0
|
CHA
|
a:HEA601
|
3.5
|
42.2
|
1.0
|
CG
|
a:HIS61
|
4.0
|
40.9
|
1.0
|
ND1
|
a:HIS378
|
4.0
|
31.0
|
1.0
|
ND1
|
a:HIS61
|
4.1
|
40.0
|
1.0
|
CG
|
a:HIS378
|
4.1
|
34.9
|
1.0
|
C3A
|
a:HEA601
|
4.3
|
40.8
|
1.0
|
C2A
|
a:HEA601
|
4.3
|
38.1
|
1.0
|
C3C
|
a:HEA601
|
4.3
|
40.4
|
1.0
|
C2C
|
a:HEA601
|
4.4
|
39.8
|
1.0
|
C2D
|
a:HEA601
|
4.4
|
41.8
|
1.0
|
C3D
|
a:HEA601
|
4.4
|
38.7
|
1.0
|
C3B
|
a:HEA601
|
4.5
|
43.3
|
1.0
|
C2B
|
a:HEA601
|
4.5
|
44.0
|
1.0
|
CE1
|
a:PHE377
|
4.8
|
36.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 5w97
Go back to
Iron Binding Sites List in 5w97
Iron binding site 4 out
of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature
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 Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe602
b:33.1
occ:1.00
|
FE
|
a:HEA602
|
0.0
|
33.1
|
1.0
|
C
|
a:CMO608
|
1.9
|
36.6
|
1.0
|
NA
|
a:HEA602
|
1.9
|
28.1
|
1.0
|
NE2
|
a:HIS376
|
1.9
|
44.7
|
1.0
|
NC
|
a:HEA602
|
2.0
|
27.3
|
1.0
|
ND
|
a:HEA602
|
2.1
|
28.9
|
1.0
|
NB
|
a:HEA602
|
2.1
|
28.7
|
1.0
|
O
|
a:CMO608
|
2.8
|
33.9
|
1.0
|
CE1
|
a:HIS376
|
2.9
|
43.2
|
1.0
|
CD2
|
a:HIS376
|
3.0
|
41.1
|
1.0
|
C1A
|
a:HEA602
|
3.0
|
28.0
|
1.0
|
C1C
|
a:HEA602
|
3.0
|
29.6
|
1.0
|
C4A
|
a:HEA602
|
3.0
|
31.2
|
1.0
|
C4C
|
a:HEA602
|
3.0
|
28.6
|
1.0
|
C4D
|
a:HEA602
|
3.1
|
29.0
|
1.0
|
C4B
|
a:HEA602
|
3.1
|
27.5
|
1.0
|
C1D
|
a:HEA602
|
3.1
|
28.5
|
1.0
|
C1B
|
a:HEA602
|
3.1
|
28.2
|
1.0
|
CHA
|
a:HEA602
|
3.4
|
28.2
|
1.0
|
CHC
|
a:HEA602
|
3.4
|
27.7
|
1.0
|
CHD
|
a:HEA602
|
3.5
|
29.6
|
1.0
|
CHB
|
a:HEA602
|
3.5
|
29.4
|
1.0
|
ND1
|
a:HIS376
|
4.1
|
36.8
|
1.0
|
CG
|
a:HIS376
|
4.1
|
37.9
|
1.0
|
C3A
|
a:HEA602
|
4.2
|
30.8
|
1.0
|
C2A
|
a:HEA602
|
4.3
|
29.7
|
1.0
|
C3C
|
a:HEA602
|
4.3
|
28.4
|
1.0
|
C2C
|
a:HEA602
|
4.3
|
30.5
|
1.0
|
C3D
|
a:HEA602
|
4.4
|
29.9
|
1.0
|
C3B
|
a:HEA602
|
4.4
|
27.0
|
1.0
|
C2B
|
a:HEA602
|
4.4
|
27.3
|
1.0
|
C2D
|
a:HEA602
|
4.4
|
29.6
|
1.0
|
|
Reference:
I.Ishigami,
N.A.Zatsepin,
M.Hikita,
C.E.Conrad,
G.Nelson,
J.D.Coe,
S.Basu,
T.D.Grant,
M.H.Seaberg,
R.G.Sierra,
M.S.Hunter,
P.Fromme,
R.Fromme,
S.R.Yeh,
D.L.Rousseau.
Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature. Proc. Natl. Acad. Sci. V. 114 8011 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28698372
DOI: 10.1073/PNAS.1705628114
Page generated: Tue Aug 6 11:05:55 2024
|