Iron in PDB 3fye: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State
Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State
All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State:
1.9.3.1;
Protein crystallography data
The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 3fye
was solved by
L.Qin,
D.A.Mills,
D.A.Proshlyakov,
C.Hiser,
S.Ferguson-Miller,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.15
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.613,
131.472,
176.192,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
22.1
|
Other elements in 3fye:
The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State
(pdb code 3fye). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 3fye:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3fye
Go back to
Iron Binding Sites List in 3fye
Iron binding site 1 out
of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe567
b:26.8
occ:1.00
|
FE
|
A:HEA567
|
0.0
|
26.8
|
1.0
|
NB
|
A:HEA567
|
2.0
|
28.7
|
1.0
|
NC
|
A:HEA567
|
2.0
|
26.9
|
1.0
|
ND
|
A:HEA567
|
2.0
|
28.2
|
1.0
|
NA
|
A:HEA567
|
2.0
|
27.1
|
1.0
|
NE2
|
A:HIS102
|
2.0
|
25.6
|
1.0
|
NE2
|
A:HIS421
|
2.1
|
31.3
|
1.0
|
CE1
|
A:HIS421
|
2.9
|
30.3
|
1.0
|
CE1
|
A:HIS102
|
3.0
|
27.0
|
1.0
|
C4B
|
A:HEA567
|
3.0
|
27.1
|
1.0
|
C1B
|
A:HEA567
|
3.0
|
26.0
|
1.0
|
C1C
|
A:HEA567
|
3.0
|
26.3
|
1.0
|
C4C
|
A:HEA567
|
3.0
|
27.4
|
1.0
|
C1D
|
A:HEA567
|
3.0
|
26.7
|
1.0
|
CD2
|
A:HIS102
|
3.0
|
24.9
|
1.0
|
C4A
|
A:HEA567
|
3.0
|
27.0
|
1.0
|
C4D
|
A:HEA567
|
3.0
|
26.3
|
1.0
|
C1A
|
A:HEA567
|
3.0
|
26.5
|
1.0
|
CD2
|
A:HIS421
|
3.1
|
29.9
|
1.0
|
CHC
|
A:HEA567
|
3.4
|
25.4
|
1.0
|
CHB
|
A:HEA567
|
3.4
|
25.3
|
1.0
|
CHD
|
A:HEA567
|
3.4
|
25.6
|
1.0
|
CHA
|
A:HEA567
|
3.4
|
25.0
|
1.0
|
ND1
|
A:HIS102
|
4.1
|
24.4
|
1.0
|
ND1
|
A:HIS421
|
4.1
|
28.0
|
1.0
|
CG
|
A:HIS102
|
4.1
|
25.4
|
1.0
|
C3B
|
A:HEA567
|
4.2
|
26.7
|
1.0
|
C2B
|
A:HEA567
|
4.2
|
27.4
|
1.0
|
CG
|
A:HIS421
|
4.2
|
29.9
|
1.0
|
C2D
|
A:HEA567
|
4.2
|
26.7
|
1.0
|
C3C
|
A:HEA567
|
4.2
|
26.4
|
1.0
|
C3D
|
A:HEA567
|
4.2
|
26.9
|
1.0
|
C2C
|
A:HEA567
|
4.2
|
26.9
|
1.0
|
C3A
|
A:HEA567
|
4.3
|
26.6
|
1.0
|
C2A
|
A:HEA567
|
4.3
|
27.6
|
1.0
|
CG2
|
A:THR48
|
4.5
|
25.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 3fye
Go back to
Iron Binding Sites List in 3fye
Iron binding site 2 out
of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe568
b:38.1
occ:1.00
|
FE
|
A:HEA568
|
0.0
|
38.1
|
1.0
|
ND
|
A:HEA568
|
2.0
|
32.2
|
1.0
|
NC
|
A:HEA568
|
2.1
|
33.8
|
1.0
|
NB
|
A:HEA568
|
2.2
|
39.4
|
1.0
|
NA
|
A:HEA568
|
2.2
|
34.8
|
1.0
|
NE2
|
A:HIS419
|
2.2
|
32.5
|
1.0
|
C1C
|
A:HEA568
|
3.0
|
32.4
|
1.0
|
C4D
|
A:HEA568
|
3.0
|
34.9
|
1.0
|
C1D
|
A:HEA568
|
3.1
|
34.1
|
1.0
|
C4C
|
A:HEA568
|
3.1
|
32.5
|
1.0
|
C4B
|
A:HEA568
|
3.1
|
39.3
|
1.0
|
CE1
|
A:HIS419
|
3.1
|
32.6
|
1.0
|
C1A
|
A:HEA568
|
3.1
|
34.0
|
1.0
|
C4A
|
A:HEA568
|
3.2
|
34.8
|
1.0
|
C1B
|
A:HEA568
|
3.2
|
40.7
|
1.0
|
CD2
|
A:HIS419
|
3.2
|
30.8
|
1.0
|
O
|
A:HOH601
|
3.3
|
55.7
|
1.0
|
CHC
|
A:HEA568
|
3.4
|
36.2
|
1.0
|
CHA
|
A:HEA568
|
3.4
|
33.1
|
1.0
|
CHD
|
A:HEA568
|
3.5
|
33.8
|
1.0
|
CHB
|
A:HEA568
|
3.6
|
36.2
|
1.0
|
C2C
|
A:HEA568
|
4.3
|
35.9
|
1.0
|
ND1
|
A:HIS419
|
4.3
|
32.4
|
1.0
|
C3D
|
A:HEA568
|
4.3
|
32.5
|
1.0
|
C3C
|
A:HEA568
|
4.3
|
34.2
|
1.0
|
C2D
|
A:HEA568
|
4.3
|
32.4
|
1.0
|
CG
|
A:HIS419
|
4.4
|
30.5
|
1.0
|
C3B
|
A:HEA568
|
4.4
|
40.9
|
1.0
|
C2A
|
A:HEA568
|
4.4
|
34.7
|
1.0
|
C3A
|
A:HEA568
|
4.4
|
34.8
|
1.0
|
C2B
|
A:HEA568
|
4.4
|
39.3
|
1.0
|
CG1
|
A:VAL423
|
4.5
|
32.9
|
1.0
|
CA
|
A:GLY398
|
4.9
|
37.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 3fye
Go back to
Iron Binding Sites List in 3fye
Iron binding site 3 out
of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe567
b:36.6
occ:1.00
|
FE
|
C:HEA567
|
0.0
|
36.6
|
1.0
|
NB
|
C:HEA567
|
1.9
|
35.1
|
1.0
|
ND
|
C:HEA567
|
2.0
|
33.5
|
1.0
|
NC
|
C:HEA567
|
2.0
|
36.6
|
1.0
|
NA
|
C:HEA567
|
2.0
|
35.5
|
1.0
|
NE2
|
C:HIS421
|
2.0
|
37.4
|
1.0
|
NE2
|
C:HIS102
|
2.1
|
41.6
|
1.0
|
CE1
|
C:HIS421
|
2.9
|
36.4
|
1.0
|
C4B
|
C:HEA567
|
3.0
|
35.7
|
1.0
|
C1C
|
C:HEA567
|
3.0
|
35.2
|
1.0
|
C1A
|
C:HEA567
|
3.0
|
33.3
|
1.0
|
C1B
|
C:HEA567
|
3.0
|
35.8
|
1.0
|
C4D
|
C:HEA567
|
3.0
|
35.1
|
1.0
|
C1D
|
C:HEA567
|
3.0
|
35.4
|
1.0
|
C4A
|
C:HEA567
|
3.0
|
35.7
|
1.0
|
C4C
|
C:HEA567
|
3.0
|
34.8
|
1.0
|
CE1
|
C:HIS102
|
3.1
|
40.4
|
1.0
|
CD2
|
C:HIS102
|
3.1
|
41.8
|
1.0
|
CD2
|
C:HIS421
|
3.1
|
37.1
|
1.0
|
CHC
|
C:HEA567
|
3.4
|
34.6
|
1.0
|
CHA
|
C:HEA567
|
3.4
|
34.1
|
1.0
|
CHD
|
C:HEA567
|
3.4
|
35.0
|
1.0
|
CHB
|
C:HEA567
|
3.4
|
33.3
|
1.0
|
ND1
|
C:HIS421
|
4.1
|
36.1
|
1.0
|
ND1
|
C:HIS102
|
4.2
|
40.8
|
1.0
|
C3B
|
C:HEA567
|
4.2
|
35.2
|
1.0
|
CG
|
C:HIS421
|
4.2
|
37.0
|
1.0
|
CG
|
C:HIS102
|
4.2
|
41.2
|
1.0
|
C2B
|
C:HEA567
|
4.2
|
34.5
|
1.0
|
C2A
|
C:HEA567
|
4.2
|
35.3
|
1.0
|
C2D
|
C:HEA567
|
4.2
|
32.7
|
1.0
|
C3D
|
C:HEA567
|
4.2
|
34.3
|
1.0
|
C2C
|
C:HEA567
|
4.2
|
36.9
|
1.0
|
C3A
|
C:HEA567
|
4.2
|
34.7
|
1.0
|
C3C
|
C:HEA567
|
4.3
|
35.3
|
1.0
|
CG2
|
C:THR48
|
4.7
|
39.4
|
1.0
|
OG
|
C:SER425
|
5.0
|
45.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 3fye
Go back to
Iron Binding Sites List in 3fye
Iron binding site 4 out
of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe568
b:42.1
occ:1.00
|
FE
|
C:HEA568
|
0.0
|
42.1
|
1.0
|
ND
|
C:HEA568
|
2.0
|
36.3
|
1.0
|
NA
|
C:HEA568
|
2.1
|
39.9
|
1.0
|
NC
|
C:HEA568
|
2.2
|
44.4
|
1.0
|
NE2
|
C:HIS419
|
2.2
|
36.1
|
1.0
|
NB
|
C:HEA568
|
2.2
|
45.6
|
1.0
|
C4D
|
C:HEA568
|
3.0
|
39.3
|
1.0
|
C1A
|
C:HEA568
|
3.0
|
37.8
|
1.0
|
C1D
|
C:HEA568
|
3.1
|
40.2
|
1.0
|
C1C
|
C:HEA568
|
3.2
|
43.2
|
1.0
|
CE1
|
C:HIS419
|
3.2
|
38.1
|
1.0
|
C4C
|
C:HEA568
|
3.2
|
42.3
|
1.0
|
C4A
|
C:HEA568
|
3.2
|
40.9
|
1.0
|
CD2
|
C:HIS419
|
3.2
|
36.4
|
1.0
|
O
|
C:HOH1601
|
3.2
|
48.2
|
1.0
|
C4B
|
C:HEA568
|
3.2
|
46.9
|
1.0
|
C1B
|
C:HEA568
|
3.3
|
45.7
|
1.0
|
CHA
|
C:HEA568
|
3.3
|
38.5
|
1.0
|
CHD
|
C:HEA568
|
3.5
|
41.4
|
1.0
|
CHC
|
C:HEA568
|
3.5
|
44.3
|
1.0
|
CHB
|
C:HEA568
|
3.6
|
42.3
|
1.0
|
C3D
|
C:HEA568
|
4.2
|
38.1
|
1.0
|
C2D
|
C:HEA568
|
4.3
|
38.7
|
1.0
|
ND1
|
C:HIS419
|
4.3
|
38.2
|
1.0
|
C2A
|
C:HEA568
|
4.3
|
38.9
|
1.0
|
CG
|
C:HIS419
|
4.3
|
35.6
|
1.0
|
C3A
|
C:HEA568
|
4.4
|
38.7
|
1.0
|
C3C
|
C:HEA568
|
4.4
|
43.3
|
1.0
|
C2C
|
C:HEA568
|
4.4
|
44.4
|
1.0
|
C2B
|
C:HEA568
|
4.5
|
45.9
|
1.0
|
C3B
|
C:HEA568
|
4.5
|
47.6
|
1.0
|
CG1
|
C:VAL423
|
4.7
|
42.4
|
1.0
|
CA
|
C:GLY398
|
5.0
|
42.7
|
1.0
|
|
Reference:
L.Qin,
J.Liu,
D.Mills,
D.A.Proshlyakov,
C.Hiser,
S.Ferguson-Miller.
Redox Dependent Conformational Changes in Cytochrome C Oxidase Suggest A Gating Mechanism For Proton Uptake. Biochemistry V. 48 5121 2009.
ISSN: ISSN 0006-2960
PubMed: 19397279
DOI: 10.1021/BI9001387
Page generated: Sun Aug 4 10:21:06 2024
|