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Iron 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:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Copper (Cu) 6 atoms
Sodium (Na) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6juw

Go back to Iron Binding Sites List in 6juw
Iron 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 Iron with other atoms in the Fe 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:Fe601

b:26.3
occ:1.00
 FE A:HEA601 0.0 26.3 1.0
NE2 A:HIS378 2.0 25.6 1.0
ND A:HEA601 2.0 23.2 1.0
NE2 A:HIS61 2.0 25.2 1.0
NA A:HEA601 2.0 26.8 1.0
NC A:HEA601 2.0 25.0 1.0
NB A:HEA601 2.0 27.5 1.0
CE1 A:HIS378 2.9 28.7 1.0
CE1 A:HIS61 2.9 28.9 1.0
C4C A:HEA601 3.0 21.4 1.0
C4A A:HEA601 3.0 23.9 1.0
C1D A:HEA601 3.0 23.2 1.0
C1C A:HEA601 3.0 23.0 1.0
C1A A:HEA601 3.0 26.8 1.0
C4D A:HEA601 3.0 22.4 1.0
CD2 A:HIS61 3.0 28.0 1.0
CD2 A:HIS378 3.0 25.5 1.0
C4B A:HEA601 3.1 23.0 1.0
C1B A:HEA601 3.1 21.5 1.0
CHC A:HEA601 3.4 22.5 1.0
CHB A:HEA601 3.4 21.8 1.0
CHA A:HEA601 3.5 21.8 1.0
CHD A:HEA601 3.5 22.5 1.0
ND1 A:HIS378 4.1 28.3 1.0
ND1 A:HIS61 4.1 25.8 1.0
CG A:HIS378 4.1 27.2 1.0
CG A:HIS61 4.2 24.2 1.0
C3A A:HEA601 4.2 22.9 1.0
C2A A:HEA601 4.2 23.6 1.0
C3C A:HEA601 4.2 20.7 1.0
C2D A:HEA601 4.2 24.4 1.0
C2C A:HEA601 4.3 21.3 1.0
C3D A:HEA601 4.3 22.8 1.0
C3B A:HEA601 4.3 23.7 1.0
C2B A:HEA601 4.3 25.1 1.0
OG A:SER382 4.6 32.8 0.1
CE1 A:PHE377 4.8 23.8 1.0

Iron binding site 2 out of 4 in 6juw

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Iron 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 Iron with other atoms in the Fe 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
A:Fe602

b:28.1
occ:1.00
 FE A:HEA602 0.0 28.1 1.0
O A:HOH711 1.7 23.0 0.7
NA A:HEA602 2.0 23.3 1.0
NB A:HEA602 2.0 30.8 1.0
ND A:HEA602 2.0 28.0 1.0
NC A:HEA602 2.0 25.3 1.0
NE2 A:HIS376 2.1 26.5 1.0
O A:HOH711 2.3 11.7 0.1
C4A A:HEA602 3.0 26.3 1.0
C1A A:HEA602 3.0 26.4 1.0
C4D A:HEA602 3.0 26.5 1.0
C4B A:HEA602 3.0 29.8 1.0
C4C A:HEA602 3.1 23.4 1.0
C1C A:HEA602 3.1 47.1 1.0
C1B A:HEA602 3.1 26.8 1.0
C1D A:HEA602 3.1 22.4 1.0
CE1 A:HIS376 3.1 28.2 1.0
CD2 A:HIS376 3.2 26.3 1.0
CHC A:HEA602 3.4 28.1 1.0
CHA A:HEA602 3.4 23.8 1.0
CHB A:HEA602 3.5 26.4 1.0
O A:HOH803 3.6 18.1 0.1
CHD A:HEA602 3.6 24.8 1.0
O A:HOH803 3.9 25.1 0.7
C3A A:HEA602 4.2 27.2 1.0
C2A A:HEA602 4.2 27.6 1.0
C3D A:HEA602 4.2 37.6 1.0
ND1 A:HIS376 4.3 27.5 1.0
C2B A:HEA602 4.3 35.2 1.0
C3B A:HEA602 4.3 28.9 1.0
C2D A:HEA602 4.3 37.2 1.0
C3C A:HEA602 4.3 23.5 1.0
CG A:HIS376 4.3 27.5 1.0
C2C A:HEA602 4.3 46.9 1.0
CU A:CU603 4.6 29.6 1.0
CG2 A:VAL243 4.7 26.2 1.0
CG1 A:VAL380 4.9 20.2 0.1
CE1 A:HIS240 4.9 27.3 1.0

Iron binding site 3 out of 4 in 6juw

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Iron 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 Iron with other atoms in the Fe 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:Fe601

b:29.6
occ:1.00
 FE N:HEA601 0.0 29.6 1.0
NE2 N:HIS61 2.0 26.6 1.0
NE2 N:HIS378 2.0 31.2 1.0
NB N:HEA601 2.0 27.3 1.0
NC N:HEA601 2.0 26.9 1.0
ND N:HEA601 2.0 28.2 1.0
NA N:HEA601 2.0 31.7 1.0
CE1 N:HIS378 2.9 32.8 1.0
CD2 N:HIS61 2.9 29.7 1.0
C4C N:HEA601 3.0 34.0 1.0
CD2 N:HIS378 3.0 25.9 1.0
C4B N:HEA601 3.0 28.1 1.0
CE1 N:HIS61 3.0 32.7 1.0
C1B N:HEA601 3.0 29.5 1.0
C1D N:HEA601 3.0 27.0 1.0
C4A N:HEA601 3.1 30.0 1.0
C1C N:HEA601 3.1 31.0 1.0
C4D N:HEA601 3.1 26.7 1.0
C1A N:HEA601 3.1 27.4 1.0
CHD N:HEA601 3.4 31.8 1.0
CHB N:HEA601 3.4 32.5 1.0
CHC N:HEA601 3.5 28.3 1.0
CHA N:HEA601 3.5 30.8 1.0
ND1 N:HIS378 4.1 29.8 1.0
ND1 N:HIS61 4.1 27.7 1.0
CG N:HIS61 4.1 29.9 1.0
CG N:HIS378 4.1 29.2 1.0
C3C N:HEA601 4.2 27.4 1.0
C3B N:HEA601 4.2 27.5 1.0
C2C N:HEA601 4.3 29.1 1.0
C3A N:HEA601 4.3 31.2 1.0
C2B N:HEA601 4.3 34.1 1.0
C2A N:HEA601 4.3 25.8 1.0
C3D N:HEA601 4.3 24.3 1.0
C2D N:HEA601 4.3 28.8 1.0
OG N:SER382 4.7 64.0 0.2
CE1 N:PHE377 4.8 26.6 1.0

Iron binding site 4 out of 4 in 6juw

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Iron 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 Iron with other atoms in the Fe 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
N:Fe602

b:29.4
occ:1.00
 FE N:HEA602 0.0 29.4 1.0
O N:HOH717 1.7 28.8 0.8
ND N:HEA602 2.0 29.0 1.0
NC N:HEA602 2.0 28.2 1.0
NB N:HEA602 2.0 29.7 1.0
NA N:HEA602 2.1 28.8 1.0
NE2 N:HIS376 2.1 29.7 1.0
O N:HOH717 2.3 13.7 0.1
C1A N:HEA602 3.0 30.8 1.0
C4C N:HEA602 3.0 30.7 1.0
C4B N:HEA602 3.0 27.1 1.0
C1C N:HEA602 3.0 32.4 1.0
C1D N:HEA602 3.1 24.6 1.0
C1B N:HEA602 3.1 27.1 1.0
C4D N:HEA602 3.1 28.0 1.0
C4A N:HEA602 3.1 26.5 1.0
CE1 N:HIS376 3.1 32.3 1.0
CD2 N:HIS376 3.1 29.1 1.0
CHC N:HEA602 3.4 29.6 1.0
CHD N:HEA602 3.5 27.0 1.0
CHA N:HEA602 3.5 28.2 1.0
CHB N:HEA602 3.5 28.3 1.0
O N:HOH843 3.6 34.1 0.1
O N:HOH843 3.8 31.4 0.8
C3A N:HEA602 4.2 26.9 1.0
ND1 N:HIS376 4.2 29.9 1.0
C2A N:HEA602 4.2 26.8 1.0
C3C N:HEA602 4.3 28.1 1.0
C3B N:HEA602 4.3 27.4 1.0
C2B N:HEA602 4.3 27.1 1.0
C2C N:HEA602 4.3 31.2 1.0
C3D N:HEA602 4.3 27.9 1.0
CG N:HIS376 4.3 27.3 1.0
C2D N:HEA602 4.3 28.9 1.0
CU N:CU603 4.6 30.6 1.0
CG2 N:VAL243 4.8 28.1 1.0
CG1 N:VAL380 4.9 23.9 0.2
CE1 N:HIS240 4.9 28.5 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 Aug 6 23:42:27 2024

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