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Iron in PDB 5xdq: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution, PDB code: 5xdq was solved by F.J.Luo, A.Shimada, N.Hagimoto, S.Shimada, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 134.45 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.307, 205.904, 177.526, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19

Other elements in 5xdq:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 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 the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution (pdb code 5xdq). 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 Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution, PDB code: 5xdq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5xdq

Go back to Iron Binding Sites List in 5xdq
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 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 the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:27.2
occ:1.00
 FE A:HEA601 0.0 27.2 1.0
NE2 A:HIS378 1.9 24.9 1.0
NE2 A:HIS61 2.0 23.8 1.0
NA A:HEA601 2.1 27.3 1.0
NB A:HEA601 2.1 25.9 1.0
NC A:HEA601 2.1 26.4 1.0
ND A:HEA601 2.1 25.9 1.0
CE1 A:HIS378 2.9 25.5 1.0
CE1 A:HIS61 3.0 25.5 1.0
CD2 A:HIS61 3.0 25.9 1.0
CD2 A:HIS378 3.0 26.2 1.0
C4A A:HEA601 3.1 26.1 1.0
C1A A:HEA601 3.1 26.5 1.0
C1B A:HEA601 3.1 25.9 1.0
C4C A:HEA601 3.1 25.4 1.0
C1C A:HEA601 3.1 24.1 1.0
C1D A:HEA601 3.1 25.2 1.0
C4B A:HEA601 3.1 24.6 1.0
C4D A:HEA601 3.1 23.9 1.0
CHB A:HEA601 3.4 27.1 1.0
CHC A:HEA601 3.5 22.5 1.0
CHD A:HEA601 3.5 25.1 1.0
CHA A:HEA601 3.5 25.4 1.0
ND1 A:HIS378 4.0 24.9 1.0
ND1 A:HIS61 4.1 24.7 1.0
CG A:HIS378 4.1 24.4 1.0
CG A:HIS61 4.1 23.6 1.0
C3A A:HEA601 4.3 25.5 1.0
C2A A:HEA601 4.3 26.3 1.0
C2B A:HEA601 4.3 25.2 1.0
C2C A:HEA601 4.3 24.6 1.0
C3C A:HEA601 4.3 24.2 1.0
C3B A:HEA601 4.3 22.7 1.0
C2D A:HEA601 4.3 22.8 1.0
C3D A:HEA601 4.3 24.5 1.0
CE1 A:PHE377 4.9 25.8 1.0

Iron binding site 2 out of 4 in 5xdq

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Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 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 the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:27.1
occ:1.00
 FE A:HEA602 0.0 27.1 1.0
NB A:HEA602 2.1 29.1 1.0
NA A:HEA602 2.1 31.6 1.0
ND A:HEA602 2.1 25.2 1.0
NC A:HEA602 2.1 26.4 1.0
NE2 A:HIS376 2.2 26.0 1.0
O1 A:PER607 2.3 25.4 0.9
O1 A:PER607 2.3 6.5 0.1
C1A A:HEA602 3.1 25.0 1.0
C4A A:HEA602 3.1 25.3 1.0
C4B A:HEA602 3.1 25.5 1.0
C1B A:HEA602 3.1 25.2 1.0
C4D A:HEA602 3.1 23.7 1.0
C1C A:HEA602 3.1 24.5 1.0
C4C A:HEA602 3.1 23.7 1.0
C1D A:HEA602 3.1 23.0 1.0
CE1 A:HIS376 3.1 24.1 1.0
CD2 A:HIS376 3.2 24.6 1.0
CHB A:HEA602 3.4 26.1 1.0
CHC A:HEA602 3.5 25.3 1.0
CHA A:HEA602 3.5 23.4 1.0
CHD A:HEA602 3.5 21.9 1.0
O2 A:PER607 3.7 24.9 0.9
C3A A:HEA602 4.3 25.6 1.0
C3B A:HEA602 4.3 23.6 1.0
C2A A:HEA602 4.3 24.3 1.0
C3D A:HEA602 4.3 23.2 1.0
C2B A:HEA602 4.3 23.6 1.0
ND1 A:HIS376 4.3 24.6 1.0
C2C A:HEA602 4.3 24.6 1.0
C3C A:HEA602 4.3 23.5 1.0
C2D A:HEA602 4.3 22.7 1.0
CG A:HIS376 4.3 24.4 1.0
O2 A:PER607 4.6 6.5 0.1
CU A:CU603 4.8 27.2 1.0
CG2 A:VAL243 5.0 23.7 1.0

Iron binding site 3 out of 4 in 5xdq

Go back to Iron Binding Sites List in 5xdq
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 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 the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:34.1
occ:1.00
 FE N:HEA601 0.0 34.1 1.0
NE2 N:HIS378 2.0 31.2 1.0
NE2 N:HIS61 2.0 30.6 1.0
NA N:HEA601 2.1 33.9 1.0
ND N:HEA601 2.1 32.1 1.0
NB N:HEA601 2.1 33.2 1.0
NC N:HEA601 2.1 34.1 1.0
CE1 N:HIS378 2.9 30.3 1.0
CD2 N:HIS61 3.0 34.9 1.0
CE1 N:HIS61 3.0 33.4 1.0
CD2 N:HIS378 3.0 29.5 1.0
C1D N:HEA601 3.1 31.4 1.0
C1B N:HEA601 3.1 33.5 1.0
C4A N:HEA601 3.1 33.7 1.0
C1A N:HEA601 3.1 32.6 1.0
C4D N:HEA601 3.1 30.5 1.0
C4C N:HEA601 3.1 33.6 1.0
C4B N:HEA601 3.1 30.6 1.0
C1C N:HEA601 3.1 33.1 1.0
CHB N:HEA601 3.4 33.4 1.0
CHD N:HEA601 3.5 34.2 1.0
CHC N:HEA601 3.5 28.3 1.0
CHA N:HEA601 3.5 29.6 1.0
ND1 N:HIS378 4.1 30.8 1.0
ND1 N:HIS61 4.2 32.6 1.0
CG N:HIS378 4.2 30.6 1.0
CG N:HIS61 4.2 32.9 1.0
C2A N:HEA601 4.3 34.2 1.0
C3A N:HEA601 4.3 34.0 1.0
C2D N:HEA601 4.3 29.7 1.0
C2B N:HEA601 4.3 34.0 1.0
C3B N:HEA601 4.3 31.6 1.0
C3D N:HEA601 4.3 29.8 1.0
C3C N:HEA601 4.3 30.4 1.0
C2C N:HEA601 4.3 31.8 1.0
CE1 N:PHE377 4.8 32.5 1.0

Iron binding site 4 out of 4 in 5xdq

Go back to Iron Binding Sites List in 5xdq
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 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 the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:31.2
occ:1.00
 FE N:HEA602 0.0 31.2 1.0
NA N:HEA602 2.1 31.2 1.0
NC N:HEA602 2.1 29.7 1.0
ND N:HEA602 2.1 29.6 1.0
NB N:HEA602 2.1 29.8 1.0
NE2 N:HIS376 2.2 30.1 1.0
O1 N:PER608 2.2 15.0 0.1
O1 N:PER608 2.3 28.4 0.9
C4A N:HEA602 3.1 29.6 1.0
C1A N:HEA602 3.1 29.6 1.0
C1C N:HEA602 3.1 29.0 1.0
C4C N:HEA602 3.1 29.7 1.0
C4D N:HEA602 3.1 29.4 1.0
C1D N:HEA602 3.1 29.1 1.0
C4B N:HEA602 3.1 27.8 1.0
C1B N:HEA602 3.1 29.2 1.0
CD2 N:HIS376 3.2 27.6 1.0
CE1 N:HIS376 3.2 28.3 1.0
CHB N:HEA602 3.5 28.6 1.0
CHC N:HEA602 3.5 30.3 1.0
CHA N:HEA602 3.5 26.9 1.0
CHD N:HEA602 3.5 28.7 1.0
O2 N:PER608 3.7 31.7 0.9
C3A N:HEA602 4.3 29.9 1.0
C2A N:HEA602 4.3 30.5 1.0
C2C N:HEA602 4.3 29.2 1.0
C3C N:HEA602 4.3 29.0 1.0
C3D N:HEA602 4.3 27.2 1.0
C3B N:HEA602 4.3 28.1 1.0
C2D N:HEA602 4.3 28.9 1.0
C2B N:HEA602 4.3 29.0 1.0
ND1 N:HIS376 4.3 28.2 1.0
CG N:HIS376 4.3 27.8 1.0
O2 N:PER608 4.5 16.1 0.1
CU N:CU603 4.8 31.6 1.0
CG2 N:VAL243 4.9 26.7 1.0

Reference:

F.Luo, K.Shinzawa-Itoh, K.Hagimoto, A.Shimada, S.Shimada, E.Yamashita, S.Yoshikawa, T.Tsukihara. Structure of Bovine Cytochrome C Oxidase Crystallized at A Neutral pH Using A Fluorinated Detergent. Acta Crystallogr F Struct V. 73 416 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28695851
DOI: 10.1107/S2053230X17008834
Page generated: Tue Aug 6 11:39:27 2024

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