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Sodium in PDB 7ev7: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at A 50 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at A 50 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at A 50 K:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at A 50 K, PDB code: 7ev7 was solved by A.Shimada, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.74 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.539, 203.655, 177.569, 90, 90, 90
R / Rfree (%) 15.9 / 17.8

Other elements in 7ev7:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at A 50 K also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at A 50 K (pdb code 7ev7). 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 the Carbon Monoxide-Bound Fully Reduced State at A 50 K, PDB code: 7ev7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7ev7

Go back to Sodium Binding Sites List in 7ev7
Sodium binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at A 50 K


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 the Carbon Monoxide-Bound Fully Reduced State at A 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:26.8
occ:1.00
 O A:HOH871 2.3 24.3 1.0
O A:SER441 2.3 25.1 1.0
O A:GLY45 2.3 31.9 1.0
OE2 A:GLU40 2.3 30.0 1.0
O A:GLU40 2.4 23.6 1.0
CD A:GLU40 3.3 30.7 1.0
C A:GLU40 3.4 24.8 1.0
O A:HOH744 3.4 34.2 1.0
C A:GLY45 3.5 29.6 1.0
CG A:GLU40 3.5 24.5 1.0
C A:SER441 3.5 24.6 1.0
O A:HOH890 3.7 31.3 1.0
CB A:ASP442 3.9 24.1 1.0
CA A:ASP442 3.9 25.0 1.0
CA A:THR46 4.0 30.7 1.0
O A:GLN43 4.0 26.8 1.0
CG A:ASP442 4.1 24.1 1.0
OD1 A:ASP442 4.1 27.0 1.0
N A:ASP442 4.2 24.0 1.0
N A:THR46 4.2 29.7 1.0
CA A:GLU40 4.3 24.3 1.0
N A:LEU41 4.3 24.0 1.0
N A:LEU47 4.4 31.2 1.0
CA A:LEU41 4.4 23.4 1.0
OE1 A:GLU40 4.4 29.3 1.0
N A:GLY45 4.5 26.5 1.0
CB A:GLU40 4.5 22.1 1.0
CA A:GLY45 4.6 28.7 1.0
C A:THR46 4.6 33.9 1.0
CD2 A:LEU41 4.7 24.4 1.0
CA A:SER441 4.7 24.0 1.0
OD2 A:ASP442 4.8 26.1 1.0
O A:HOH722 4.9 32.4 1.0
CB A:SER441 5.0 27.6 1.0

Sodium binding site 2 out of 4 in 7ev7

Go back to Sodium Binding Sites List in 7ev7
Sodium binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at A 50 K


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 the Carbon Monoxide-Bound Fully Reduced State at A 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:809.6
occ:1.00
 O C:HOH521 2.3 142.0 1.0
NE2 C:HIS232 2.4 28.3 1.0
NE2 C:HIS148 2.5 33.5 1.0
CD C:GLU236 2.7 68.5 1.0
CG C:GLU236 2.7 45.2 1.0
CD2 C:HIS232 2.8 27.4 1.0
OE1 C:GLU236 3.0 79.2 1.0
OE2 C:GLU236 3.2 76.8 1.0
CE1 C:HIS148 3.4 38.7 1.0
CD2 C:HIS148 3.4 36.4 1.0
CE1 C:HIS232 3.7 29.1 1.0
CG C:HIS232 4.1 24.1 1.0
CB C:GLU236 4.3 25.9 1.0
ND1 C:HIS148 4.5 37.9 1.0
ND1 C:HIS232 4.5 25.7 1.0
CG C:HIS148 4.5 34.1 1.0
O C:HOH470 4.6 40.4 1.0
O C:HOH416 4.6 29.5 1.0
CG C:MET152 4.7 29.7 1.0
SD C:MET152 4.7 37.0 1.0
O C:HIS232 4.8 24.6 1.0

Sodium binding site 3 out of 4 in 7ev7

Go back to Sodium Binding Sites List in 7ev7
Sodium binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at A 50 K


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 the Carbon Monoxide-Bound Fully Reduced State at A 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na606

b:31.6
occ:1.00
 O N:HOH869 2.3 28.8 1.0
O N:GLY45 2.3 33.5 1.0
OE2 N:GLU40 2.3 36.6 1.0
O N:SER441 2.3 31.6 1.0
O N:GLU40 2.4 30.9 1.0
CD N:GLU40 3.2 34.4 1.0
C N:GLU40 3.4 32.7 1.0
O N:HOH813 3.5 35.7 1.0
CG N:GLU40 3.5 29.1 1.0
C N:GLY45 3.5 37.4 1.0
C N:SER441 3.5 30.5 1.0
CB N:ASP442 3.9 29.2 1.0
O N:HOH875 3.9 36.1 1.0
CA N:ASP442 3.9 30.4 1.0
O N:GLN43 4.0 31.3 1.0
CA N:THR46 4.0 36.8 1.0
CG N:ASP442 4.1 30.7 1.0
OD1 N:ASP442 4.2 32.3 1.0
N N:ASP442 4.2 29.9 1.0
N N:LEU41 4.2 29.9 1.0
N N:THR46 4.2 36.7 1.0
CA N:GLU40 4.3 31.9 1.0
CA N:LEU41 4.3 29.5 1.0
OE1 N:GLU40 4.4 35.6 1.0
N N:GLY45 4.5 32.1 1.0
N N:LEU47 4.5 36.0 1.0
CB N:GLU40 4.5 28.9 1.0
CD2 N:LEU41 4.6 26.4 1.0
CA N:GLY45 4.6 36.9 1.0
CA N:SER441 4.7 30.2 1.0
C N:THR46 4.7 38.9 1.0
OD2 N:ASP442 4.8 32.0 1.0
CB N:SER441 5.0 35.2 1.0
O N:HOH811 5.0 39.0 1.0

Sodium binding site 4 out of 4 in 7ev7

Go back to Sodium Binding Sites List in 7ev7
Sodium binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at A 50 K


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 the Carbon Monoxide-Bound Fully Reduced State at A 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na302

b:17.5
occ:0.30
 O P:HOH505 1.7 41.8 1.0
NE2 P:HIS148 2.2 34.3 1.0
NE2 P:HIS232 2.4 24.8 1.0
CD2 P:HIS148 3.1 35.5 1.0
CD2 P:HIS232 3.1 27.0 1.0
CE1 P:HIS148 3.2 40.8 1.0
CD P:GLU236 3.3 59.4 1.0
CG P:GLU236 3.3 39.6 1.0
CE1 P:HIS232 3.5 26.9 1.0
OE2 P:GLU236 3.6 61.9 1.0
OE1 P:GLU236 3.7 66.1 1.0
SD P:MET152 4.1 39.1 1.0
CG P:MET152 4.1 31.4 1.0
CG P:HIS148 4.2 34.0 1.0
ND1 P:HIS148 4.3 38.8 1.0
CG P:HIS232 4.3 24.0 1.0
ND1 P:HIS232 4.5 24.5 1.0
O P:HOH466 4.7 49.3 1.0
CB P:GLU236 4.8 27.8 1.0
CE P:MET152 4.9 30.9 1.0
O P:HOH412 5.0 27.3 1.0

Reference:

A.Shimada, K.Shinzawa-Itoh, K.Muramoto, T.Tsukihara, S.Yoshikawa. Structure of Co-Bound Fully Reduced State of Bovine Heart Cytochrome C Oxidase To Be Published.
Page generated: Tue Oct 8 16:44:09 2024

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