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Iron in PDB 5zco: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days

Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days

All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days:
1.9.3.1;

Protein crystallography data

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days, PDB code: 5zco was solved by A.Shimada, K.Hatano, H.Tadehara, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.379, 206.655, 177.589, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 18.9

Other elements in 5zco:

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days 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 Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days (pdb code 5zco). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days, PDB code: 5zco:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5zco

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Iron binding site 1 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:26.1
occ:1.00
FE A:HEA601 0.0 26.1 1.0
NE2 A:HIS61 2.0 22.9 1.0
NC A:HEA601 2.0 27.0 1.0
NE2 A:HIS378 2.0 23.9 1.0
ND A:HEA601 2.0 23.6 1.0
NB A:HEA601 2.0 26.8 1.0
NA A:HEA601 2.0 26.8 1.0
CE1 A:HIS378 2.9 24.4 1.0
CE1 A:HIS61 3.0 24.5 1.0
CD2 A:HIS61 3.0 22.9 1.0
C1B A:HEA601 3.0 25.2 1.0
C4C A:HEA601 3.0 25.1 1.0
C1D A:HEA601 3.0 23.7 1.0
C4D A:HEA601 3.0 22.1 1.0
C4A A:HEA601 3.1 27.5 1.0
C4B A:HEA601 3.1 25.2 1.0
C1C A:HEA601 3.1 26.4 1.0
C1A A:HEA601 3.1 27.0 1.0
CD2 A:HIS378 3.1 23.9 1.0
CHB A:HEA601 3.4 28.5 1.0
CHD A:HEA601 3.5 24.6 1.0
CHC A:HEA601 3.5 22.9 1.0
CHA A:HEA601 3.5 23.1 1.0
ND1 A:HIS378 4.1 24.8 1.0
CG A:HIS61 4.1 24.0 1.0
ND1 A:HIS61 4.1 24.1 1.0
CG A:HIS378 4.2 22.8 1.0
C2D A:HEA601 4.2 21.6 1.0
C3B A:HEA601 4.3 24.4 1.0
C3A A:HEA601 4.3 24.8 1.0
C3D A:HEA601 4.3 23.3 1.0
C2A A:HEA601 4.3 26.9 1.0
C3C A:HEA601 4.3 24.7 1.0
C2B A:HEA601 4.3 26.1 1.0
C2C A:HEA601 4.3 27.1 1.0
OG A:SER382 4.8 28.8 0.2
CE1 A:PHE377 4.9 26.7 1.0

Iron binding site 2 out of 6 in 5zco

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Iron binding site 2 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:25.1
occ:0.70
FE A:HEA602 0.0 25.1 0.7
FE A:HEA602 0.9 24.9 0.3
ND A:HEA602 1.4 24.7 0.3
NC A:HEA602 1.7 24.7 0.3
NC A:HEA602 2.0 24.2 0.7
NB A:HEA602 2.0 27.1 0.7
N1 A:AZI607 2.0 25.9 0.7
NE2 A:HIS376 2.1 28.0 1.0
NA A:HEA602 2.1 24.4 0.7
ND A:HEA602 2.1 28.0 0.7
C1D A:HEA602 2.2 26.0 0.3
N3 A:AZI606 2.4 21.5 0.3
C4C A:HEA602 2.4 26.7 0.3
CHD A:HEA602 2.6 25.9 0.3
C4D A:HEA602 2.6 24.7 0.3
NA A:HEA602 2.7 25.6 0.3
NB A:HEA602 2.9 26.9 0.3
C1C A:HEA602 3.0 24.9 0.3
N2 A:AZI607 3.0 27.9 0.7
C1C A:HEA602 3.0 22.2 0.7
C4D A:HEA602 3.0 25.8 0.7
C4C A:HEA602 3.0 24.0 0.7
C4A A:HEA602 3.1 22.9 0.7
C4B A:HEA602 3.1 25.5 0.7
CD2 A:HIS376 3.1 28.6 1.0
CE1 A:HIS376 3.1 28.3 1.0
C1B A:HEA602 3.1 26.4 0.7
C1D A:HEA602 3.1 23.3 0.7
C1A A:HEA602 3.1 22.1 0.7
N2 A:AZI606 3.3 25.0 0.3
C1A A:HEA602 3.4 25.3 0.3
CHA A:HEA602 3.4 24.6 0.3
N1 A:AZI607 3.4 21.9 0.3
CHB A:HEA602 3.4 21.4 0.7
CHD A:HEA602 3.5 21.5 0.7
CHC A:HEA602 3.5 22.7 0.7
C2D A:HEA602 3.5 24.6 0.3
CHA A:HEA602 3.5 23.3 0.7
C4B A:HEA602 3.7 26.2 0.3
C3D A:HEA602 3.7 25.4 0.3
C3C A:HEA602 3.7 26.6 0.3
CHC A:HEA602 3.8 26.5 0.3
C4A A:HEA602 3.8 25.4 0.3
C1B A:HEA602 3.9 25.4 0.3
N2 A:AZI607 4.0 30.1 0.3
C2C A:HEA602 4.0 25.9 0.3
N3 A:AZI607 4.2 29.2 0.7
C3D A:HEA602 4.2 23.9 0.7
C3C A:HEA602 4.2 23.2 0.7
C2D A:HEA602 4.2 24.6 0.7
C2C A:HEA602 4.2 24.1 0.7
C3B A:HEA602 4.3 25.0 0.7
ND1 A:HIS376 4.3 27.3 1.0
CG A:HIS376 4.3 28.7 1.0
C3A A:HEA602 4.3 23.6 0.7
C2B A:HEA602 4.3 26.1 0.7
C2A A:HEA602 4.3 21.5 0.7
CHB A:HEA602 4.3 25.5 0.3
N1 A:AZI606 4.5 26.3 0.3
C2A A:HEA602 4.7 24.5 0.3
CG1 A:VAL380 4.7 22.0 0.2
CMD A:HEA602 4.7 22.5 0.3
N3 A:AZI607 4.8 26.1 0.3
C3A A:HEA602 4.9 25.5 0.3
C3B A:HEA602 4.9 24.4 0.3
CG2 A:VAL243 5.0 24.3 1.0
CAC A:HEA602 5.0 26.3 0.3

Iron binding site 3 out of 6 in 5zco

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Iron binding site 3 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:24.9
occ:0.30
FE A:HEA602 0.0 24.9 0.3
FE A:HEA602 0.9 25.1 0.7
NB A:HEA602 1.4 27.1 0.7
NA A:HEA602 1.6 24.4 0.7
NA A:HEA602 2.0 25.6 0.3
NB A:HEA602 2.1 26.9 0.3
ND A:HEA602 2.1 24.7 0.3
NC A:HEA602 2.1 24.7 0.3
NE2 A:HIS376 2.1 28.0 1.0
N3 A:AZI606 2.2 21.5 0.3
N1 A:AZI607 2.2 25.9 0.7
C1B A:HEA602 2.2 26.4 0.7
C4A A:HEA602 2.3 22.9 0.7
CHB A:HEA602 2.5 21.4 0.7
NC A:HEA602 2.7 24.2 0.7
C4B A:HEA602 2.7 25.5 0.7
ND A:HEA602 2.8 28.0 0.7
N2 A:AZI606 2.8 25.0 0.3
C1A A:HEA602 2.9 22.1 0.7
CE1 A:HIS376 3.0 28.3 1.0
C4A A:HEA602 3.0 25.4 0.3
C1A A:HEA602 3.0 25.3 0.3
C1B A:HEA602 3.0 25.4 0.3
C1D A:HEA602 3.1 26.0 0.3
C4D A:HEA602 3.1 24.7 0.3
C4B A:HEA602 3.1 26.2 0.3
C4C A:HEA602 3.1 26.7 0.3
C1C A:HEA602 3.1 24.9 0.3
CD2 A:HIS376 3.1 28.6 1.0
N2 A:AZI607 3.4 27.9 0.7
CHB A:HEA602 3.4 25.5 0.3
C1C A:HEA602 3.4 22.2 0.7
CHA A:HEA602 3.4 24.6 0.3
CHC A:HEA602 3.5 26.5 0.3
CHD A:HEA602 3.5 25.9 0.3
CHC A:HEA602 3.5 22.7 0.7
C2B A:HEA602 3.6 26.1 0.7
C4D A:HEA602 3.6 25.8 0.7
N1 A:AZI607 3.6 21.9 0.3
C3A A:HEA602 3.7 23.6 0.7
CHA A:HEA602 3.7 23.3 0.7
C3B A:HEA602 3.7 25.0 0.7
C4C A:HEA602 3.9 24.0 0.7
N1 A:AZI606 3.9 26.3 0.3
C2A A:HEA602 4.0 21.5 0.7
C1D A:HEA602 4.0 23.3 0.7
C2A A:HEA602 4.2 24.5 0.3
C3A A:HEA602 4.2 25.5 0.3
ND1 A:HIS376 4.2 27.3 1.0
C2B A:HEA602 4.2 25.9 0.3
C3B A:HEA602 4.3 24.4 0.3
C3D A:HEA602 4.3 25.4 0.3
CG A:HIS376 4.3 28.7 1.0
C2D A:HEA602 4.3 24.6 0.3
C2C A:HEA602 4.3 25.9 0.3
C3C A:HEA602 4.3 26.6 0.3
CHD A:HEA602 4.4 21.5 0.7
N2 A:AZI607 4.4 30.1 0.3
CA A:GLY355 4.5 26.7 1.0
N3 A:AZI607 4.6 29.2 0.7
C2C A:HEA602 4.8 24.1 0.7
C3D A:HEA602 4.9 23.9 0.7
CMB A:HEA602 4.9 26.9 0.7
C3C A:HEA602 5.0 23.2 0.7
CMA A:HEA602 5.0 24.9 0.7

Iron binding site 4 out of 6 in 5zco

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Iron binding site 4 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:30.6
occ:1.00
FE N:HEA602 0.0 30.6 1.0
NE2 N:HIS61 1.9 27.2 1.0
NC N:HEA602 2.0 30.1 1.0
NA N:HEA602 2.0 32.6 1.0
NE2 N:HIS378 2.0 28.3 1.0
NB N:HEA602 2.0 30.6 1.0
ND N:HEA602 2.0 28.4 1.0
CD2 N:HIS61 2.9 31.1 1.0
CE1 N:HIS378 2.9 27.3 1.0
C1B N:HEA602 3.0 32.0 1.0
CE1 N:HIS61 3.0 33.1 1.0
C1D N:HEA602 3.0 30.1 1.0
C4C N:HEA602 3.0 31.4 1.0
C4A N:HEA602 3.0 31.2 1.0
C4B N:HEA602 3.0 33.1 1.0
C1A N:HEA602 3.0 29.9 1.0
C4D N:HEA602 3.0 28.3 1.0
CD2 N:HIS378 3.0 27.3 1.0
C1C N:HEA602 3.1 32.1 1.0
CHB N:HEA602 3.4 32.9 1.0
CHD N:HEA602 3.4 31.8 1.0
CHA N:HEA602 3.5 29.3 1.0
CHC N:HEA602 3.5 29.0 1.0
ND1 N:HIS378 4.1 28.4 1.0
CG N:HIS61 4.1 29.8 1.0
ND1 N:HIS61 4.2 29.8 1.0
CG N:HIS378 4.2 28.4 1.0
C3B N:HEA602 4.2 31.5 1.0
C2A N:HEA602 4.2 28.6 1.0
C2B N:HEA602 4.2 31.8 1.0
C3A N:HEA602 4.2 31.6 1.0
C2C N:HEA602 4.2 29.1 1.0
C3C N:HEA602 4.3 30.3 1.0
C3D N:HEA602 4.3 25.7 1.0
C2D N:HEA602 4.3 28.0 1.0
CE1 N:PHE377 4.9 30.8 1.0
OG N:SER382 4.9 37.1 0.2

Iron binding site 5 out of 6 in 5zco

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Iron binding site 5 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:26.8
occ:0.70
FE N:HEA603 0.0 26.8 0.7
FE N:HEA603 1.0 30.9 0.3
ND N:HEA603 1.5 29.1 0.3
NC N:HEA603 1.6 27.5 0.3
NB N:HEA603 2.0 25.0 0.7
N1 N:AZI608 2.0 30.7 0.7
ND N:HEA603 2.0 29.4 0.7
NC N:HEA603 2.0 28.3 0.7
NA N:HEA603 2.1 26.1 0.7
NE2 N:HIS376 2.1 31.1 1.0
C4C N:HEA603 2.2 28.5 0.3
C1D N:HEA603 2.2 29.2 0.3
N3 N:AZI607 2.2 23.2 0.3
CHD N:HEA603 2.4 27.2 0.3
N2 N:AZI608 2.7 25.8 0.7
C4D N:HEA603 2.7 28.9 0.3
NA N:HEA603 2.8 30.3 0.3
C1C N:HEA603 2.8 29.2 0.3
C1B N:HEA603 3.0 27.5 0.7
C4C N:HEA603 3.0 26.9 0.7
C1C N:HEA603 3.0 28.3 0.7
NB N:HEA603 3.0 30.9 0.3
C4D N:HEA603 3.1 28.8 0.7
C4B N:HEA603 3.1 26.4 0.7
C1D N:HEA603 3.1 26.3 0.7
C1A N:HEA603 3.1 24.4 0.7
C4A N:HEA603 3.1 25.2 0.7
CD2 N:HIS376 3.1 31.4 1.0
CE1 N:HIS376 3.1 29.6 1.0
N2 N:AZI607 3.2 23.1 0.3
CHB N:HEA603 3.4 25.7 0.7
CHA N:HEA603 3.4 25.0 0.7
CHD N:HEA603 3.5 25.4 0.7
C3C N:HEA603 3.5 27.5 0.3
C2D N:HEA603 3.5 30.5 0.3
C1A N:HEA603 3.5 30.0 0.3
CHA N:HEA603 3.5 28.6 0.3
CHC N:HEA603 3.5 26.9 0.7
N3 N:AZI608 3.7 33.6 0.7
C3D N:HEA603 3.7 31.0 0.3
CHC N:HEA603 3.8 28.8 0.3
C2C N:HEA603 3.8 29.7 0.3
C4B N:HEA603 3.8 29.4 0.3
C4A N:HEA603 3.9 31.1 0.3
N1 N:AZI608 4.0 22.9 0.3
C1B N:HEA603 4.2 29.2 0.3
C3C N:HEA603 4.2 28.0 0.7
C2C N:HEA603 4.2 30.1 0.7
C2B N:HEA603 4.2 26.0 0.7
C3B N:HEA603 4.3 25.5 0.7
N1 N:AZI607 4.3 22.4 0.3
C2D N:HEA603 4.3 27.8 0.7
C3D N:HEA603 4.3 26.1 0.7
ND1 N:HIS376 4.3 30.7 1.0
C3A N:HEA603 4.3 24.3 0.7
CG N:HIS376 4.3 30.1 1.0
C2A N:HEA603 4.3 26.5 0.7
CHB N:HEA603 4.5 29.5 0.3
N2 N:AZI608 4.7 22.4 0.3
CG1 N:VAL380 4.7 29.6 0.2
CAC N:HEA603 4.8 27.1 0.3
CMD N:HEA603 4.8 30.5 0.3
C2A N:HEA603 4.8 29.6 0.3
CU N:CU604 5.0 31.0 1.0

Iron binding site 6 out of 6 in 5zco

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Iron binding site 6 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 2 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:30.9
occ:0.30
FE N:HEA603 0.0 30.9 0.3
FE N:HEA603 1.0 26.8 0.7
NB N:HEA603 1.4 25.0 0.7
NA N:HEA603 1.6 26.1 0.7
N3 N:AZI607 1.9 23.2 0.3
NC N:HEA603 2.0 27.5 0.3
NA N:HEA603 2.0 30.3 0.3
C1B N:HEA603 2.1 27.5 0.7
ND N:HEA603 2.1 29.1 0.3
NB N:HEA603 2.2 30.9 0.3
N1 N:AZI608 2.2 30.7 0.7
C4A N:HEA603 2.2 25.2 0.7
NE2 N:HIS376 2.2 31.1 1.0
CHB N:HEA603 2.3 25.7 0.7
N2 N:AZI607 2.6 23.1 0.3
C4B N:HEA603 2.8 26.4 0.7
NC N:HEA603 2.8 28.3 0.7
C1A N:HEA603 2.9 24.4 0.7
ND N:HEA603 2.9 29.4 0.7
C1C N:HEA603 3.0 29.2 0.3
C4C N:HEA603 3.0 28.5 0.3
C4A N:HEA603 3.0 31.1 0.3
N2 N:AZI608 3.0 25.8 0.7
C1A N:HEA603 3.0 30.0 0.3
CE1 N:HIS376 3.1 29.6 1.0
C1D N:HEA603 3.1 29.2 0.3
C4D N:HEA603 3.1 28.9 0.3
C4B N:HEA603 3.2 29.4 0.3
C1B N:HEA603 3.2 29.2 0.3
CD2 N:HIS376 3.2 31.4 1.0
C2B N:HEA603 3.4 26.0 0.7
CHD N:HEA603 3.4 27.2 0.3
CHB N:HEA603 3.5 29.5 0.3
CHC N:HEA603 3.5 28.8 0.3
CHA N:HEA603 3.5 28.6 0.3
C1C N:HEA603 3.5 28.3 0.7
C3A N:HEA603 3.6 24.3 0.7
N1 N:AZI607 3.6 22.4 0.3
CHA N:HEA603 3.6 25.0 0.7
CHC N:HEA603 3.6 26.9 0.7
C4D N:HEA603 3.7 28.8 0.7
C3B N:HEA603 3.7 25.5 0.7
C2A N:HEA603 3.9 26.5 0.7
C4C N:HEA603 4.0 26.9 0.7
C1D N:HEA603 4.1 26.3 0.7
N3 N:AZI608 4.1 33.6 0.7
C2C N:HEA603 4.2 29.7 0.3
C3A N:HEA603 4.2 31.1 0.3
C3C N:HEA603 4.2 27.5 0.3
C2A N:HEA603 4.2 29.6 0.3
ND1 N:HIS376 4.2 30.7 1.0
CG N:HIS376 4.3 30.1 1.0
C2B N:HEA603 4.3 29.3 0.3
C2D N:HEA603 4.4 30.5 0.3
C3D N:HEA603 4.4 31.0 0.3
C3B N:HEA603 4.4 29.9 0.3
CA N:GLY355 4.5 33.1 1.0
N1 N:AZI608 4.5 22.9 0.3
CHD N:HEA603 4.5 25.4 0.7
CMB N:HEA603 4.7 27.4 0.7
CMA N:HEA603 4.8 26.9 0.7
C2C N:HEA603 4.9 30.1 0.7
CU N:CU604 5.0 31.0 1.0
OMA N:HEA603 5.0 26.9 0.7
C3D N:HEA603 5.0 26.1 0.7

Reference:

A.Shimada, K.Hatano, H.Tadehara, N.Yano, K.Shinzawa-Itoh, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. X-Ray Structural Analyses of Azide-Bound Cytochromecoxidases Reveal That the H-Pathway Is Critically Important For the Proton-Pumping Activity. J. Biol. Chem. V. 293 14868 2018.
ISSN: ESSN 1083-351X
PubMed: 30077971
DOI: 10.1074/JBC.RA118.003123
Page generated: Sun Dec 13 16:19:11 2020

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