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Iron in PDB 5b3s: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K), PDB code: 5b3s was solved by J.Baba, A.Shimada, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.491, 203.303, 177.484, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 17.4

Other elements in 5b3s:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) (pdb code 5b3s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K), PDB code: 5b3s:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5b3s

Go back to Iron Binding Sites List in 5b3s
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:22.4
occ:1.00
 FE A:HEA601 0.0 22.4 1.0
NE2 A:HIS378 1.9 16.8 1.0
NE2 A:HIS61 1.9 18.6 1.0
NC A:HEA601 2.0 22.3 1.0
NB A:HEA601 2.1 22.9 1.0
NA A:HEA601 2.1 22.2 1.0
ND A:HEA601 2.1 22.9 1.0
CE1 A:HIS378 2.8 24.3 1.0
CE1 A:HIS61 2.9 20.8 1.0
CD2 A:HIS378 3.0 23.4 1.0
CD2 A:HIS61 3.0 24.4 1.0
C1B A:HEA601 3.1 22.2 1.0
C1A A:HEA601 3.1 20.4 1.0
C4A A:HEA601 3.1 21.4 1.0
C1C A:HEA601 3.1 20.0 1.0
C4C A:HEA601 3.1 21.5 1.0
C1D A:HEA601 3.1 18.9 1.0
C4B A:HEA601 3.1 22.5 1.0
C4D A:HEA601 3.1 20.1 1.0
CHB A:HEA601 3.4 22.2 1.0
CHC A:HEA601 3.5 21.2 1.0
CHD A:HEA601 3.5 20.5 1.0
CHA A:HEA601 3.5 22.5 1.0
ND1 A:HIS378 4.0 21.4 1.0
ND1 A:HIS61 4.0 21.6 1.0
CG A:HIS378 4.1 20.7 1.0
CG A:HIS61 4.1 20.4 1.0
C3A A:HEA601 4.2 22.6 1.0
C2A A:HEA601 4.3 23.6 1.0
C3C A:HEA601 4.3 19.8 1.0
C2C A:HEA601 4.3 20.5 1.0
C3B A:HEA601 4.3 20.3 1.0
C3D A:HEA601 4.3 21.9 1.0
C2B A:HEA601 4.3 22.4 1.0
C2D A:HEA601 4.3 19.0 1.0
CE1 A:PHE377 4.8 20.8 1.0

Iron binding site 2 out of 4 in 5b3s

Go back to Iron Binding Sites List in 5b3s
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:22.5
occ:1.00
 FE A:HEA602 0.0 22.5 1.0
NB A:HEA602 2.0 22.9 1.0
NC A:HEA602 2.0 25.7 1.0
NA A:HEA602 2.1 24.3 1.0
ND A:HEA602 2.1 20.4 1.0
NE2 A:HIS376 2.1 26.2 1.0
C A:CMO606 2.9 29.8 1.0
C1C A:HEA602 3.0 21.5 1.0
C4A A:HEA602 3.0 19.9 1.0
C4C A:HEA602 3.0 19.5 1.0
C4B A:HEA602 3.1 19.9 1.0
C1B A:HEA602 3.1 20.2 1.0
C4D A:HEA602 3.1 19.4 1.0
C1A A:HEA602 3.1 19.0 1.0
C1D A:HEA602 3.1 20.4 1.0
CD2 A:HIS376 3.2 22.5 1.0
CE1 A:HIS376 3.2 23.6 1.0
CHB A:HEA602 3.4 20.2 1.0
CHC A:HEA602 3.5 20.8 1.0
CHD A:HEA602 3.5 20.0 1.0
CHA A:HEA602 3.5 21.6 1.0
O A:CMO606 3.5 30.7 1.0
C3C A:HEA602 4.3 19.8 1.0
C3B A:HEA602 4.3 21.0 1.0
C3A A:HEA602 4.3 22.3 1.0
C2D A:HEA602 4.3 19.6 1.0
C2A A:HEA602 4.3 20.7 1.0
C2C A:HEA602 4.3 20.5 1.0
C3D A:HEA602 4.3 19.4 1.0
ND1 A:HIS376 4.3 23.3 1.0
C2B A:HEA602 4.3 21.7 1.0
CG A:HIS376 4.4 22.2 1.0
CU A:CU603 4.9 23.2 1.0
CA A:GLY355 5.0 22.5 1.0
CG2 A:VAL380 5.0 22.5 1.0

Iron binding site 3 out of 4 in 5b3s

Go back to Iron Binding Sites List in 5b3s
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:25.2
occ:1.00
 FE N:HEA601 0.0 25.2 1.0
NE2 N:HIS61 1.9 21.6 1.0
NE2 N:HIS378 2.0 20.9 1.0
NB N:HEA601 2.0 26.4 1.0
NC N:HEA601 2.0 24.0 1.0
ND N:HEA601 2.1 25.3 1.0
NA N:HEA601 2.1 26.6 1.0
CE1 N:HIS61 2.9 24.1 1.0
CD2 N:HIS61 3.0 27.4 1.0
CE1 N:HIS378 3.0 23.4 1.0
CD2 N:HIS378 3.0 24.6 1.0
C1B N:HEA601 3.0 23.9 1.0
C4B N:HEA601 3.0 25.6 1.0
C1D N:HEA601 3.1 22.4 1.0
C1A N:HEA601 3.1 24.3 1.0
C4A N:HEA601 3.1 26.2 1.0
C4C N:HEA601 3.1 24.6 1.0
C1C N:HEA601 3.1 24.6 1.0
C4D N:HEA601 3.1 23.9 1.0
CHB N:HEA601 3.4 24.8 1.0
CHD N:HEA601 3.5 23.9 1.0
CHC N:HEA601 3.5 24.0 1.0
CHA N:HEA601 3.5 23.9 1.0
ND1 N:HIS61 4.1 24.1 1.0
ND1 N:HIS378 4.1 25.5 1.0
CG N:HIS61 4.1 23.2 1.0
CG N:HIS378 4.2 21.4 1.0
C2A N:HEA601 4.2 27.1 1.0
C3A N:HEA601 4.3 25.2 1.0
C3B N:HEA601 4.3 24.8 1.0
C2B N:HEA601 4.3 24.9 1.0
C2D N:HEA601 4.3 22.1 1.0
C3D N:HEA601 4.3 24.1 1.0
C3C N:HEA601 4.3 23.3 1.0
C2C N:HEA601 4.3 22.6 1.0
CE1 N:PHE377 4.8 25.1 1.0

Iron binding site 4 out of 4 in 5b3s

Go back to Iron Binding Sites List in 5b3s
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:24.2
occ:1.00
 FE N:HEA602 0.0 24.2 1.0
NC N:HEA602 2.0 25.5 1.0
NB N:HEA602 2.1 23.4 1.0
ND N:HEA602 2.1 22.7 1.0
NA N:HEA602 2.1 25.8 1.0
NE2 N:HIS376 2.2 27.0 1.0
C N:CMO606 3.0 29.7 1.0
C1C N:HEA602 3.0 21.6 1.0
C4C N:HEA602 3.0 21.6 1.0
C1D N:HEA602 3.0 20.8 1.0
C1B N:HEA602 3.1 21.9 1.0
C4B N:HEA602 3.1 20.5 1.0
C4D N:HEA602 3.1 22.6 1.0
C1A N:HEA602 3.1 23.0 1.0
C4A N:HEA602 3.1 21.6 1.0
CE1 N:HIS376 3.2 24.6 1.0
CD2 N:HIS376 3.2 21.8 1.0
CHB N:HEA602 3.4 20.5 1.0
CHD N:HEA602 3.5 21.0 1.0
CHA N:HEA602 3.5 22.5 1.0
CHC N:HEA602 3.5 21.7 1.0
O N:CMO606 3.5 31.4 1.0
C2D N:HEA602 4.3 24.5 1.0
C2C N:HEA602 4.3 21.6 1.0
C3D N:HEA602 4.3 21.7 1.0
C3C N:HEA602 4.3 21.6 1.0
C3B N:HEA602 4.3 22.4 1.0
C2B N:HEA602 4.3 22.1 1.0
C2A N:HEA602 4.3 21.4 1.0
C3A N:HEA602 4.4 22.5 1.0
ND1 N:HIS376 4.4 24.6 1.0
CG N:HIS376 4.4 20.7 1.0
CU N:CU603 4.9 24.7 1.0
CA N:GLY355 5.0 24.0 1.0
CG2 N:VAL380 5.0 24.3 1.0

Reference:

A.Shimada, J.Baba, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Tsukihara. Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed-Valence State at 1.68 Angstrom Resolution (50 K) To Be Published.
Page generated: Mon Aug 5 19:59:56 2024

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