Iron in PDB 2yev: Structure of CAA3-Type Cytochrome Oxidase
Enzymatic activity of Structure of CAA3-Type Cytochrome Oxidase
All present enzymatic activity of Structure of CAA3-Type Cytochrome Oxidase:
1.9.3.1;
Protein crystallography data
The structure of Structure of CAA3-Type Cytochrome Oxidase, PDB code: 2yev
was solved by
J.A.Lyons,
D.Aragao,
T.Soulimane,
M.Caffrey,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
77.18 /
2.36
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
127.250,
76.030,
300.267,
90.00,
92.21,
90.00
|
R / Rfree (%)
|
17.1 /
21.8
|
Other elements in 2yev:
The structure of Structure of CAA3-Type Cytochrome Oxidase also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of CAA3-Type Cytochrome Oxidase
(pdb code 2yev). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Structure of CAA3-Type Cytochrome Oxidase, PDB code: 2yev:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 2yev
Go back to
Iron Binding Sites List in 2yev
Iron binding site 1 out
of 6 in the Structure of CAA3-Type Cytochrome Oxidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1015
b:30.9
occ:1.00
|
FE
|
A:HAS1015
|
0.0
|
30.9
|
1.0
|
NE2
|
A:HIS73
|
2.0
|
30.2
|
1.0
|
ND
|
A:HAS1015
|
2.0
|
30.4
|
1.0
|
NE2
|
A:HIS387
|
2.1
|
28.9
|
1.0
|
NC
|
A:HAS1015
|
2.1
|
36.0
|
1.0
|
NA
|
A:HAS1015
|
2.1
|
34.6
|
1.0
|
NB
|
A:HAS1015
|
2.2
|
30.1
|
1.0
|
CD2
|
A:HIS73
|
3.0
|
40.2
|
1.0
|
CD2
|
A:HIS387
|
3.0
|
33.0
|
1.0
|
C4C
|
A:HAS1015
|
3.0
|
33.5
|
1.0
|
C4D
|
A:HAS1015
|
3.0
|
26.3
|
1.0
|
C1D
|
A:HAS1015
|
3.0
|
38.4
|
1.0
|
C1C
|
A:HAS1015
|
3.1
|
37.2
|
1.0
|
CE1
|
A:HIS73
|
3.1
|
36.2
|
1.0
|
C4A
|
A:HAS1015
|
3.1
|
33.5
|
1.0
|
C1A
|
A:HAS1015
|
3.1
|
25.6
|
1.0
|
CE1
|
A:HIS387
|
3.1
|
44.2
|
1.0
|
C4B
|
A:HAS1015
|
3.2
|
30.8
|
1.0
|
C1B
|
A:HAS1015
|
3.2
|
35.6
|
1.0
|
CHD
|
A:HAS1015
|
3.4
|
24.9
|
1.0
|
CHA
|
A:HAS1015
|
3.4
|
28.5
|
1.0
|
CHC
|
A:HAS1015
|
3.5
|
33.7
|
1.0
|
CHB
|
A:HAS1015
|
3.5
|
27.0
|
1.0
|
CG
|
A:HIS73
|
4.1
|
31.6
|
1.0
|
CG
|
A:HIS387
|
4.2
|
38.9
|
1.0
|
ND1
|
A:HIS73
|
4.2
|
33.7
|
1.0
|
ND1
|
A:HIS387
|
4.2
|
36.0
|
1.0
|
C2D
|
A:HAS1015
|
4.3
|
35.0
|
1.0
|
C3C
|
A:HAS1015
|
4.3
|
35.3
|
1.0
|
C3D
|
A:HAS1015
|
4.3
|
39.7
|
1.0
|
C2C
|
A:HAS1015
|
4.3
|
37.9
|
1.0
|
C3A
|
A:HAS1015
|
4.4
|
35.1
|
1.0
|
C2A
|
A:HAS1015
|
4.4
|
32.4
|
1.0
|
C3B
|
A:HAS1015
|
4.4
|
32.9
|
1.0
|
C2B
|
A:HAS1015
|
4.5
|
25.0
|
1.0
|
|
Iron binding site 2 out
of 6 in 2yev
Go back to
Iron Binding Sites List in 2yev
Iron binding site 2 out
of 6 in the Structure of CAA3-Type Cytochrome Oxidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1016
b:31.7
occ:1.00
|
FE
|
A:HAS1016
|
0.0
|
31.7
|
1.0
|
NA
|
A:HAS1016
|
2.1
|
32.0
|
1.0
|
ND
|
A:HAS1016
|
2.1
|
40.2
|
1.0
|
NC
|
A:HAS1016
|
2.1
|
28.5
|
1.0
|
NB
|
A:HAS1016
|
2.2
|
30.2
|
1.0
|
O
|
A:HOH2077
|
2.2
|
25.9
|
1.0
|
NE2
|
A:HIS385
|
2.3
|
28.6
|
1.0
|
C1D
|
A:HAS1016
|
3.1
|
48.0
|
1.0
|
C1A
|
A:HAS1016
|
3.1
|
38.2
|
1.0
|
C4D
|
A:HAS1016
|
3.1
|
35.1
|
1.0
|
C4A
|
A:HAS1016
|
3.1
|
44.1
|
1.0
|
C4C
|
A:HAS1016
|
3.1
|
33.7
|
1.0
|
C1C
|
A:HAS1016
|
3.1
|
35.7
|
1.0
|
C1B
|
A:HAS1016
|
3.1
|
38.2
|
1.0
|
C4B
|
A:HAS1016
|
3.2
|
42.2
|
1.0
|
CD2
|
A:HIS385
|
3.2
|
35.1
|
1.0
|
CE1
|
A:HIS385
|
3.2
|
33.6
|
1.0
|
CHA
|
A:HAS1016
|
3.4
|
27.8
|
1.0
|
CHB
|
A:HAS1016
|
3.4
|
30.8
|
1.0
|
CHD
|
A:HAS1016
|
3.5
|
29.9
|
1.0
|
CHC
|
A:HAS1016
|
3.5
|
26.0
|
1.0
|
C2D
|
A:HAS1016
|
4.3
|
38.4
|
1.0
|
O
|
A:HOH2076
|
4.3
|
49.4
|
1.0
|
ND1
|
A:HIS385
|
4.4
|
33.0
|
1.0
|
C3A
|
A:HAS1016
|
4.4
|
38.1
|
1.0
|
CG
|
A:HIS385
|
4.4
|
41.9
|
1.0
|
C3C
|
A:HAS1016
|
4.4
|
35.3
|
1.0
|
C3D
|
A:HAS1016
|
4.4
|
40.8
|
1.0
|
C2A
|
A:HAS1016
|
4.4
|
22.1
|
1.0
|
C2C
|
A:HAS1016
|
4.4
|
35.4
|
1.0
|
C2B
|
A:HAS1016
|
4.4
|
29.1
|
1.0
|
C3B
|
A:HAS1016
|
4.5
|
34.0
|
1.0
|
CU
|
A:CU1017
|
4.9
|
37.6
|
1.0
|
|
Iron binding site 3 out
of 6 in 2yev
Go back to
Iron Binding Sites List in 2yev
Iron binding site 3 out
of 6 in the Structure of CAA3-Type Cytochrome Oxidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe587
b:35.1
occ:1.00
|
FE
|
B:HEC587
|
0.0
|
35.1
|
1.0
|
NA
|
B:HEC587
|
2.0
|
35.9
|
1.0
|
NC
|
B:HEC587
|
2.0
|
37.1
|
1.0
|
ND
|
B:HEC587
|
2.0
|
32.4
|
1.0
|
NB
|
B:HEC587
|
2.0
|
34.3
|
1.0
|
NE2
|
B:HIS251
|
2.1
|
48.6
|
1.0
|
SD
|
B:MET303
|
2.4
|
37.3
|
1.0
|
CD2
|
B:HIS251
|
3.0
|
37.0
|
1.0
|
C4D
|
B:HEC587
|
3.0
|
39.6
|
1.0
|
C1A
|
B:HEC587
|
3.0
|
45.8
|
1.0
|
C1C
|
B:HEC587
|
3.0
|
29.3
|
1.0
|
CE1
|
B:HIS251
|
3.0
|
41.6
|
1.0
|
C4B
|
B:HEC587
|
3.1
|
29.6
|
1.0
|
C4C
|
B:HEC587
|
3.1
|
37.2
|
1.0
|
C1D
|
B:HEC587
|
3.1
|
35.1
|
1.0
|
C4A
|
B:HEC587
|
3.1
|
52.1
|
1.0
|
C1B
|
B:HEC587
|
3.1
|
37.4
|
1.0
|
CHA
|
B:HEC587
|
3.4
|
25.9
|
1.0
|
CHC
|
B:HEC587
|
3.4
|
33.2
|
1.0
|
CHD
|
B:HEC587
|
3.4
|
40.7
|
1.0
|
CG
|
B:MET303
|
3.5
|
43.1
|
1.0
|
CHB
|
B:HEC587
|
3.5
|
34.9
|
1.0
|
CE
|
B:MET303
|
3.5
|
32.5
|
1.0
|
ND1
|
B:HIS251
|
4.1
|
50.8
|
1.0
|
CG
|
B:HIS251
|
4.2
|
46.5
|
1.0
|
CB
|
B:MET303
|
4.2
|
28.7
|
1.0
|
C2A
|
B:HEC587
|
4.3
|
48.2
|
1.0
|
C3D
|
B:HEC587
|
4.3
|
23.8
|
1.0
|
C2C
|
B:HEC587
|
4.3
|
30.6
|
1.0
|
C3C
|
B:HEC587
|
4.3
|
31.9
|
1.0
|
C3B
|
B:HEC587
|
4.3
|
38.2
|
1.0
|
C3A
|
B:HEC587
|
4.3
|
48.0
|
1.0
|
C2B
|
B:HEC587
|
4.3
|
22.8
|
1.0
|
C2D
|
B:HEC587
|
4.3
|
32.7
|
1.0
|
NE1
|
B:TRP290
|
5.0
|
39.2
|
1.0
|
|
Iron binding site 4 out
of 6 in 2yev
Go back to
Iron Binding Sites List in 2yev
Iron binding site 4 out
of 6 in the Structure of CAA3-Type Cytochrome Oxidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1015
b:42.4
occ:1.00
|
FE
|
D:HAS1015
|
0.0
|
42.4
|
1.0
|
NE2
|
D:HIS387
|
2.0
|
34.0
|
1.0
|
NC
|
D:HAS1015
|
2.1
|
78.6
|
1.0
|
NE2
|
D:HIS73
|
2.1
|
33.0
|
1.0
|
NA
|
D:HAS1015
|
2.1
|
70.9
|
1.0
|
ND
|
D:HAS1015
|
2.1
|
49.9
|
1.0
|
NB
|
D:HAS1015
|
2.2
|
58.6
|
1.0
|
CD2
|
D:HIS387
|
2.9
|
47.9
|
1.0
|
CD2
|
D:HIS73
|
3.0
|
50.9
|
1.0
|
C4C
|
D:HAS1015
|
3.0
|
72.2
|
1.0
|
CE1
|
D:HIS387
|
3.1
|
48.3
|
1.0
|
C4A
|
D:HAS1015
|
3.1
|
51.2
|
1.0
|
C1D
|
D:HAS1015
|
3.1
|
44.5
|
1.0
|
C1C
|
D:HAS1015
|
3.1
|
68.9
|
1.0
|
C1A
|
D:HAS1015
|
3.1
|
46.2
|
1.0
|
C4D
|
D:HAS1015
|
3.1
|
62.3
|
1.0
|
C1B
|
D:HAS1015
|
3.1
|
48.5
|
1.0
|
CE1
|
D:HIS73
|
3.2
|
44.2
|
1.0
|
C4B
|
D:HAS1015
|
3.2
|
68.8
|
1.0
|
CHD
|
D:HAS1015
|
3.4
|
51.4
|
1.0
|
CHA
|
D:HAS1015
|
3.4
|
62.0
|
1.0
|
CHB
|
D:HAS1015
|
3.4
|
55.4
|
1.0
|
CHC
|
D:HAS1015
|
3.5
|
63.6
|
1.0
|
CG
|
D:HIS387
|
4.1
|
39.4
|
1.0
|
ND1
|
D:HIS387
|
4.1
|
49.1
|
1.0
|
CG
|
D:HIS73
|
4.2
|
43.3
|
1.0
|
ND1
|
D:HIS73
|
4.2
|
46.3
|
1.0
|
C3C
|
D:HAS1015
|
4.3
|
74.5
|
1.0
|
C2C
|
D:HAS1015
|
4.4
|
68.8
|
1.0
|
C2D
|
D:HAS1015
|
4.4
|
61.2
|
1.0
|
C3A
|
D:HAS1015
|
4.4
|
55.5
|
1.0
|
C2A
|
D:HAS1015
|
4.4
|
65.5
|
1.0
|
C3D
|
D:HAS1015
|
4.4
|
53.3
|
1.0
|
C2B
|
D:HAS1015
|
4.4
|
58.4
|
1.0
|
C3B
|
D:HAS1015
|
4.5
|
70.3
|
1.0
|
|
Iron binding site 5 out
of 6 in 2yev
Go back to
Iron Binding Sites List in 2yev
Iron binding site 5 out
of 6 in the Structure of CAA3-Type Cytochrome Oxidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1016
b:42.5
occ:1.00
|
FE
|
D:HAS1016
|
0.0
|
42.5
|
1.0
|
NC
|
D:HAS1016
|
2.1
|
32.8
|
1.0
|
ND
|
D:HAS1016
|
2.1
|
37.5
|
1.0
|
NA
|
D:HAS1016
|
2.1
|
29.3
|
1.0
|
NB
|
D:HAS1016
|
2.1
|
40.4
|
1.0
|
NE2
|
D:HIS385
|
2.3
|
56.9
|
1.0
|
O
|
D:HOH2054
|
2.7
|
35.8
|
1.0
|
C1D
|
D:HAS1016
|
3.0
|
57.7
|
1.0
|
C1C
|
D:HAS1016
|
3.0
|
24.3
|
1.0
|
C4C
|
D:HAS1016
|
3.1
|
41.1
|
1.0
|
C1A
|
D:HAS1016
|
3.1
|
39.8
|
1.0
|
C4A
|
D:HAS1016
|
3.1
|
46.3
|
1.0
|
C4D
|
D:HAS1016
|
3.1
|
36.9
|
1.0
|
C1B
|
D:HAS1016
|
3.1
|
42.3
|
1.0
|
C4B
|
D:HAS1016
|
3.1
|
35.8
|
1.0
|
CE1
|
D:HIS385
|
3.2
|
49.2
|
1.0
|
CD2
|
D:HIS385
|
3.3
|
52.9
|
1.0
|
CHB
|
D:HAS1016
|
3.4
|
33.2
|
1.0
|
CHD
|
D:HAS1016
|
3.4
|
32.2
|
1.0
|
CHC
|
D:HAS1016
|
3.4
|
47.3
|
1.0
|
CHA
|
D:HAS1016
|
3.4
|
28.8
|
1.0
|
C2D
|
D:HAS1016
|
4.3
|
32.8
|
1.0
|
C3C
|
D:HAS1016
|
4.3
|
27.1
|
1.0
|
C2C
|
D:HAS1016
|
4.3
|
42.2
|
1.0
|
ND1
|
D:HIS385
|
4.3
|
48.2
|
1.0
|
C3A
|
D:HAS1016
|
4.4
|
26.8
|
1.0
|
CG
|
D:HIS385
|
4.4
|
45.9
|
1.0
|
C3D
|
D:HAS1016
|
4.4
|
62.8
|
1.0
|
C2B
|
D:HAS1016
|
4.4
|
33.9
|
1.0
|
C2A
|
D:HAS1016
|
4.4
|
39.9
|
1.0
|
C3B
|
D:HAS1016
|
4.4
|
49.7
|
1.0
|
CU
|
D:CU1017
|
4.8
|
42.6
|
1.0
|
O
|
D:HOH2053
|
4.9
|
50.7
|
1.0
|
|
Iron binding site 6 out
of 6 in 2yev
Go back to
Iron Binding Sites List in 2yev
Iron binding site 6 out
of 6 in the Structure of CAA3-Type Cytochrome Oxidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe587
b:48.3
occ:1.00
|
FE
|
E:HEC587
|
0.0
|
48.3
|
1.0
|
NC
|
E:HEC587
|
2.0
|
62.2
|
1.0
|
NE2
|
E:HIS251
|
2.1
|
41.3
|
1.0
|
ND
|
E:HEC587
|
2.1
|
91.2
|
1.0
|
NA
|
E:HEC587
|
2.1
|
81.9
|
1.0
|
NB
|
E:HEC587
|
2.1
|
78.1
|
1.0
|
SD
|
E:MET303
|
2.4
|
48.5
|
1.0
|
CD2
|
E:HIS251
|
3.0
|
42.4
|
1.0
|
C4C
|
E:HEC587
|
3.0
|
65.2
|
1.0
|
C1D
|
E:HEC587
|
3.0
|
44.2
|
1.0
|
C4A
|
E:HEC587
|
3.1
|
80.3
|
1.0
|
C1C
|
E:HEC587
|
3.1
|
66.8
|
1.0
|
C1B
|
E:HEC587
|
3.1
|
63.8
|
1.0
|
C4B
|
E:HEC587
|
3.1
|
56.3
|
1.0
|
CE1
|
E:HIS251
|
3.1
|
55.1
|
1.0
|
C4D
|
E:HEC587
|
3.1
|
58.5
|
1.0
|
C1A
|
E:HEC587
|
3.1
|
76.6
|
1.0
|
CHD
|
E:HEC587
|
3.3
|
57.7
|
1.0
|
CHB
|
E:HEC587
|
3.4
|
80.2
|
1.0
|
CG
|
E:MET303
|
3.5
|
48.7
|
1.0
|
CE
|
E:MET303
|
3.5
|
52.4
|
1.0
|
CHC
|
E:HEC587
|
3.5
|
54.4
|
1.0
|
CHA
|
E:HEC587
|
3.5
|
47.8
|
1.0
|
CG
|
E:HIS251
|
4.1
|
47.5
|
1.0
|
ND1
|
E:HIS251
|
4.2
|
52.6
|
1.0
|
CB
|
E:MET303
|
4.2
|
41.7
|
1.0
|
C3C
|
E:HEC587
|
4.2
|
70.9
|
1.0
|
C2C
|
E:HEC587
|
4.3
|
55.8
|
1.0
|
C2D
|
E:HEC587
|
4.3
|
73.8
|
1.0
|
C3A
|
E:HEC587
|
4.3
|
69.4
|
1.0
|
C3B
|
E:HEC587
|
4.3
|
55.4
|
1.0
|
C2B
|
E:HEC587
|
4.3
|
69.6
|
1.0
|
C3D
|
E:HEC587
|
4.3
|
54.1
|
1.0
|
C2A
|
E:HEC587
|
4.3
|
57.0
|
1.0
|
|
Reference:
J.A.Lyons,
D.Aragao,
O.Slattery,
A.V.Pisliakov,
T.Soulimane,
M.Caffrey.
Structural Insights Into Electron Transfer in CAA3-Type Cytochrome Oxidases. Nature V. 487 514 2012.
ISSN: ISSN 0028-0836
PubMed: 22763450
DOI: 10.1038/NATURE11182
Page generated: Sun Aug 4 05:31:40 2024
|