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Iron in PDB 5xdx: Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx 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) 40.00 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.044, 205.691, 177.797, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.3

Other elements in 5xdx:

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution (pdb code 5xdx). 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5xdx

Go back to Iron Binding Sites List in 5xdx
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:27.5
occ:1.00
 FE A:HEA601 0.0 27.5 1.0
NE2 A:HIS61 1.9 24.7 1.0
NE2 A:HIS378 2.0 25.2 1.0
NB A:HEA601 2.1 29.5 1.0
NA A:HEA601 2.1 28.2 1.0
NC A:HEA601 2.1 30.1 1.0
ND A:HEA601 2.1 27.8 1.0
CE1 A:HIS61 2.9 26.9 1.0
CD2 A:HIS61 2.9 25.4 1.0
CE1 A:HIS378 3.0 26.8 1.0
CD2 A:HIS378 3.0 25.9 1.0
C4B A:HEA601 3.1 28.9 1.0
C1B A:HEA601 3.1 29.4 1.0
C4A A:HEA601 3.1 28.9 1.0
C4C A:HEA601 3.1 28.7 1.0
C1A A:HEA601 3.1 28.0 1.0
C1D A:HEA601 3.1 27.7 1.0
C4D A:HEA601 3.1 26.8 1.0
C1C A:HEA601 3.1 28.8 1.0
CHB A:HEA601 3.4 28.2 1.0
CHD A:HEA601 3.4 27.9 1.0
CHA A:HEA601 3.5 26.8 1.0
CHC A:HEA601 3.5 26.9 1.0
ND1 A:HIS61 4.1 26.0 1.0
CG A:HIS61 4.1 25.7 1.0
ND1 A:HIS378 4.1 26.0 1.0
CG A:HIS378 4.2 25.2 1.0
C3B A:HEA601 4.2 29.6 1.0
C3A A:HEA601 4.3 28.0 1.0
C2B A:HEA601 4.3 29.3 1.0
C2A A:HEA601 4.3 27.9 1.0
C3C A:HEA601 4.3 28.4 1.0
C2D A:HEA601 4.3 26.2 1.0
C3D A:HEA601 4.3 27.1 1.0
C2C A:HEA601 4.3 28.5 1.0
OG A:SER382 4.6 39.1 1.0

Iron binding site 2 out of 4 in 5xdx

Go back to Iron Binding Sites List in 5xdx
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:30.8
occ:1.00
 FE A:HEA602 0.0 30.8 1.0
NB A:HEA602 2.1 28.1 1.0
NA A:HEA602 2.1 28.4 1.0
NC A:HEA602 2.1 28.1 1.0
ND A:HEA602 2.1 28.3 1.0
NE2 A:HIS376 2.2 30.1 1.0
C4B A:HEA602 3.1 28.3 1.0
C1A A:HEA602 3.1 28.1 1.0
C1B A:HEA602 3.1 28.2 1.0
C4A A:HEA602 3.1 28.5 1.0
C4D A:HEA602 3.1 28.4 1.0
C1C A:HEA602 3.1 28.3 1.0
C4C A:HEA602 3.1 27.9 1.0
C1D A:HEA602 3.1 27.9 1.0
CE1 A:HIS376 3.2 29.7 1.0
CD2 A:HIS376 3.2 28.8 1.0
CHB A:HEA602 3.4 28.7 1.0
CHA A:HEA602 3.5 27.1 1.0
CHC A:HEA602 3.5 27.5 1.0
CHD A:HEA602 3.5 26.9 1.0
C2B A:HEA602 4.3 27.9 1.0
C3B A:HEA602 4.3 28.3 1.0
C3A A:HEA602 4.3 28.2 1.0
C2A A:HEA602 4.3 28.2 1.0
C3D A:HEA602 4.3 28.3 1.0
C2C A:HEA602 4.3 29.4 1.0
C3C A:HEA602 4.3 28.0 1.0
C2D A:HEA602 4.3 27.5 1.0
ND1 A:HIS376 4.3 29.2 1.0
CG A:HIS376 4.4 29.6 1.0
CG1 A:VAL380 4.7 31.8 1.0
CG2 A:VAL243 5.0 25.6 1.0

Iron binding site 3 out of 4 in 5xdx

Go back to Iron Binding Sites List in 5xdx
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:40.0
occ:1.00
 FE N:HEA601 0.0 40.0 1.0
NE2 N:HIS61 2.0 38.5 1.0
NE2 N:HIS378 2.0 39.6 1.0
NB N:HEA601 2.1 42.4 1.0
ND N:HEA601 2.1 40.0 1.0
NC N:HEA601 2.1 39.1 1.0
NA N:HEA601 2.1 42.2 1.0
CD2 N:HIS61 2.9 38.9 1.0
CD2 N:HIS378 3.0 39.2 1.0
CE1 N:HIS378 3.0 40.0 1.0
CE1 N:HIS61 3.0 39.3 1.0
C4B N:HEA601 3.1 42.3 1.0
C1B N:HEA601 3.1 43.1 1.0
C1D N:HEA601 3.1 39.4 1.0
C1A N:HEA601 3.1 41.5 1.0
C4C N:HEA601 3.1 39.6 1.0
C4A N:HEA601 3.1 42.1 1.0
C4D N:HEA601 3.1 39.7 1.0
C1C N:HEA601 3.1 40.2 1.0
CHB N:HEA601 3.5 42.8 1.0
CHD N:HEA601 3.5 38.3 1.0
CHC N:HEA601 3.5 40.0 1.0
CHA N:HEA601 3.5 39.8 1.0
CG N:HIS61 4.1 39.6 1.0
ND1 N:HIS378 4.1 39.8 1.0
ND1 N:HIS61 4.1 39.6 1.0
CG N:HIS378 4.2 39.6 1.0
C3B N:HEA601 4.2 43.7 1.0
C2B N:HEA601 4.3 43.7 1.0
C2D N:HEA601 4.3 38.1 1.0
C2A N:HEA601 4.3 42.3 1.0
C3A N:HEA601 4.3 42.6 1.0
C3D N:HEA601 4.3 38.3 1.0
C3C N:HEA601 4.3 38.4 1.0
C2C N:HEA601 4.3 39.3 1.0
OG N:SER382 4.5 55.2 1.0
CE1 N:PHE377 5.0 39.9 1.0

Iron binding site 4 out of 4 in 5xdx

Go back to Iron Binding Sites List in 5xdx
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:39.3
occ:1.00
 FE N:HEA602 0.0 39.3 1.0
NC N:HEA602 2.1 36.5 1.0
NA N:HEA602 2.1 37.5 1.0
NB N:HEA602 2.1 35.5 1.0
ND N:HEA602 2.1 36.7 1.0
NE2 N:HIS376 2.2 39.4 1.0
C1A N:HEA602 3.1 37.0 1.0
C1C N:HEA602 3.1 36.8 1.0
C4C N:HEA602 3.1 37.6 1.0
C4D N:HEA602 3.1 36.7 1.0
C4B N:HEA602 3.1 35.7 1.0
C4A N:HEA602 3.1 37.0 1.0
C1D N:HEA602 3.1 36.7 1.0
C1B N:HEA602 3.1 36.5 1.0
CE1 N:HIS376 3.2 37.5 1.0
CD2 N:HIS376 3.2 37.7 1.0
CHA N:HEA602 3.4 35.8 1.0
CHC N:HEA602 3.5 36.0 1.0
CHD N:HEA602 3.5 36.8 1.0
CHB N:HEA602 3.5 36.9 1.0
C2C N:HEA602 4.3 37.3 1.0
C2A N:HEA602 4.3 37.1 1.0
C3C N:HEA602 4.3 37.3 1.0
C3A N:HEA602 4.3 36.7 1.0
C3D N:HEA602 4.3 36.8 1.0
C2D N:HEA602 4.3 36.8 1.0
C3B N:HEA602 4.3 36.1 1.0
C2B N:HEA602 4.3 36.4 1.0
ND1 N:HIS376 4.3 37.9 1.0
CG N:HIS376 4.4 38.0 1.0
CG2 N:VAL380 4.7 46.4 1.0
CG2 N:VAL243 4.9 32.0 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 in the Ligand-Free Reduced State at Neutral pH. Acta Crystallogr F Struct V. 74 92 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29400318
DOI: 10.1107/S2053230X17018532
Page generated: Tue Aug 6 11:39:27 2024

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