Sodium in PDB 6juw: Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution
Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution
All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution:
1.9.3.1;
Protein crystallography data
The structure of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw
was solved by
A.Shimada,
K.Muramoto,
K.Shinzawa-Itoh,
S.Yoshikawa,
T.Tsukihara,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.88 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
182.217,
204.650,
177.397,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.7 /
18.8
|
Other elements in 6juw:
The structure of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution
(pdb code 6juw). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6juw
Go back to
Sodium Binding Sites List in 6juw
Sodium binding site 1 out
of 4 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na605
b:29.0
occ:1.00
|
O
|
A:HOH869
|
2.2
|
27.6
|
1.0
|
OE1
|
A:GLU40
|
2.3
|
34.5
|
1.0
|
O
|
A:SER441
|
2.3
|
31.6
|
1.0
|
O
|
A:GLY45
|
2.3
|
35.3
|
1.0
|
O
|
A:GLU40
|
2.4
|
30.6
|
1.0
|
CD
|
A:GLU40
|
3.2
|
39.8
|
1.0
|
C
|
A:GLU40
|
3.4
|
39.1
|
1.0
|
O
|
A:HOH825
|
3.4
|
40.2
|
1.0
|
C
|
A:GLY45
|
3.5
|
36.7
|
1.0
|
C
|
A:SER441
|
3.5
|
32.7
|
1.0
|
CG
|
A:GLU40
|
3.5
|
26.7
|
1.0
|
CA
|
A:ASP442
|
3.9
|
29.6
|
1.0
|
O
|
A:GLN43
|
3.9
|
32.6
|
1.0
|
CB
|
A:ASP442
|
4.0
|
28.4
|
1.0
|
CA
|
A:THR46
|
4.0
|
36.2
|
1.0
|
CG
|
A:ASP442
|
4.1
|
29.8
|
1.0
|
OD1
|
A:ASP442
|
4.1
|
33.0
|
1.0
|
N
|
A:ASP442
|
4.2
|
28.9
|
1.0
|
N
|
A:THR46
|
4.2
|
34.9
|
1.0
|
CA
|
A:GLU40
|
4.2
|
27.4
|
1.0
|
N
|
A:LEU41
|
4.3
|
30.3
|
1.0
|
N
|
A:LEU47
|
4.3
|
34.9
|
1.0
|
CA
|
A:LEU41
|
4.4
|
28.8
|
1.0
|
OE2
|
A:GLU40
|
4.4
|
32.5
|
1.0
|
N
|
A:GLY45
|
4.5
|
30.9
|
1.0
|
CB
|
A:GLU40
|
4.5
|
26.6
|
1.0
|
CA
|
A:GLY45
|
4.6
|
36.8
|
1.0
|
C
|
A:THR46
|
4.6
|
39.3
|
1.0
|
CA
|
A:SER441
|
4.7
|
28.8
|
1.0
|
CD2
|
A:LEU41
|
4.7
|
27.1
|
1.0
|
OD2
|
A:ASP442
|
4.9
|
32.8
|
1.0
|
CB
|
A:SER441
|
5.0
|
33.0
|
1.0
|
|
Sodium binding site 2 out
of 4 in 6juw
Go back to
Sodium Binding Sites List in 6juw
Sodium binding site 2 out
of 4 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na301
b:22.1
occ:1.00
|
O
|
C:HOH412
|
1.9
|
47.1
|
1.0
|
OE2
|
C:GLU236
|
2.0
|
0.6
|
1.0
|
NE2
|
C:HIS148
|
2.0
|
36.5
|
1.0
|
NE2
|
C:HIS232
|
2.1
|
31.7
|
1.0
|
CD
|
C:GLU236
|
2.5
|
48.2
|
1.0
|
CE1
|
C:HIS148
|
2.9
|
52.2
|
1.0
|
CD2
|
C:HIS232
|
3.0
|
34.5
|
1.0
|
CD2
|
C:HIS148
|
3.1
|
35.2
|
1.0
|
OE1
|
C:GLU236
|
3.1
|
72.4
|
1.0
|
CE1
|
C:HIS232
|
3.2
|
31.5
|
1.0
|
CG
|
C:GLU236
|
3.4
|
85.3
|
1.0
|
ND1
|
C:HIS148
|
4.1
|
42.5
|
1.0
|
CG
|
C:HIS148
|
4.2
|
36.5
|
1.0
|
CG
|
C:HIS232
|
4.2
|
28.5
|
1.0
|
CG
|
C:MET152
|
4.3
|
40.6
|
1.0
|
ND1
|
C:HIS232
|
4.3
|
30.1
|
1.0
|
SD
|
C:MET152
|
4.3
|
49.4
|
1.0
|
CB
|
C:GLU236
|
4.7
|
29.9
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6juw
Go back to
Sodium Binding Sites List in 6juw
Sodium binding site 3 out
of 4 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Na605
b:34.1
occ:1.00
|
O
|
N:HOH844
|
2.2
|
33.1
|
1.0
|
OE1
|
N:GLU40
|
2.3
|
38.2
|
1.0
|
O
|
N:GLY45
|
2.3
|
38.4
|
1.0
|
O
|
N:SER441
|
2.3
|
31.2
|
1.0
|
O
|
N:GLU40
|
2.4
|
37.3
|
1.0
|
CD
|
N:GLU40
|
3.2
|
45.1
|
1.0
|
C
|
N:GLU40
|
3.4
|
35.1
|
1.0
|
O
|
N:HOH734
|
3.4
|
42.6
|
1.0
|
C
|
N:GLY45
|
3.5
|
50.1
|
1.0
|
CG
|
N:GLU40
|
3.5
|
32.7
|
1.0
|
C
|
N:SER441
|
3.5
|
34.2
|
1.0
|
CA
|
N:ASP442
|
3.9
|
29.6
|
1.0
|
CB
|
N:ASP442
|
3.9
|
32.5
|
1.0
|
O
|
N:GLN43
|
4.0
|
37.0
|
1.0
|
OD1
|
N:ASP442
|
4.0
|
38.0
|
1.0
|
CG
|
N:ASP442
|
4.0
|
37.8
|
1.0
|
CA
|
N:THR46
|
4.1
|
40.4
|
1.0
|
N
|
N:ASP442
|
4.2
|
31.4
|
1.0
|
N
|
N:LEU41
|
4.2
|
31.7
|
1.0
|
N
|
N:THR46
|
4.2
|
40.2
|
1.0
|
CA
|
N:GLU40
|
4.3
|
32.0
|
1.0
|
CA
|
N:LEU41
|
4.3
|
35.1
|
1.0
|
OE2
|
N:GLU40
|
4.4
|
36.6
|
1.0
|
N
|
N:GLY45
|
4.4
|
41.0
|
1.0
|
N
|
N:LEU47
|
4.5
|
45.1
|
1.0
|
CB
|
N:GLU40
|
4.5
|
29.1
|
1.0
|
CA
|
N:GLY45
|
4.6
|
41.1
|
1.0
|
CD2
|
N:LEU41
|
4.6
|
31.8
|
1.0
|
CA
|
N:SER441
|
4.6
|
30.2
|
1.0
|
C
|
N:THR46
|
4.7
|
56.5
|
1.0
|
OD2
|
N:ASP442
|
4.7
|
37.4
|
1.0
|
CB
|
N:SER441
|
4.9
|
39.7
|
1.0
|
C
|
N:PRO44
|
5.0
|
36.5
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6juw
Go back to
Sodium Binding Sites List in 6juw
Sodium binding site 4 out
of 4 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Na301
b:22.3
occ:1.00
|
O
|
P:HOH403
|
1.7
|
46.8
|
1.0
|
OE2
|
P:GLU236
|
2.0
|
0.8
|
1.0
|
NE2
|
P:HIS148
|
2.1
|
34.4
|
1.0
|
NE2
|
P:HIS232
|
2.2
|
31.8
|
1.0
|
CD
|
P:GLU236
|
2.8
|
56.3
|
1.0
|
CD2
|
P:HIS232
|
2.9
|
30.2
|
1.0
|
CD2
|
P:HIS148
|
3.0
|
32.6
|
1.0
|
CE1
|
P:HIS148
|
3.1
|
49.8
|
1.0
|
CG
|
P:GLU236
|
3.2
|
65.0
|
1.0
|
CE1
|
P:HIS232
|
3.3
|
30.5
|
1.0
|
OE1
|
P:GLU236
|
3.7
|
73.2
|
1.0
|
SD
|
P:MET152
|
4.2
|
49.9
|
1.0
|
ND1
|
P:HIS148
|
4.2
|
40.8
|
1.0
|
CG
|
P:HIS232
|
4.2
|
31.0
|
1.0
|
CG
|
P:MET152
|
4.2
|
38.8
|
1.0
|
CG
|
P:HIS148
|
4.2
|
32.8
|
1.0
|
C1
|
P:EDO316
|
4.2
|
52.2
|
1.0
|
ND1
|
P:HIS232
|
4.3
|
31.1
|
1.0
|
C2
|
P:EDO316
|
4.4
|
94.7
|
1.0
|
CB
|
P:GLU236
|
4.7
|
29.8
|
1.0
|
|
Reference:
A.Shimada,
Y.Etoh,
R.Kitoh-Fujisawa,
A.Sasaki,
K.Shinzawa-Itoh,
T.Hiromoto,
E.Yamashita,
K.Muramoto,
T.Tsukihara,
S.Yoshikawa.
X-Ray Structures of Catalytic Intermediates of Cytochromecoxidase Provide Insights Into Its O2-Activation and Unidirectional Proton-Pump Mechanisms. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32165497
DOI: 10.1074/JBC.RA119.009596
Page generated: Tue Oct 8 11:28:42 2024
|