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Iron in PDB 5z86: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days

Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days

All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days:
1.9.3.1;

Protein crystallography data

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days, PDB code: 5z86 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 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.490, 206.292, 177.617, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 19.6

Other elements in 5z86:

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 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 20 Mm Azide Solution For 3 Days (pdb code 5z86). 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 20 Mm Azide Solution For 3 Days, PDB code: 5z86:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5z86

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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 20 Mm Azide Solution For 3 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 20 Mm Azide Solution For 3 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:26.5
occ:1.00
FE A:HEA601 0.0 26.5 1.0
NE2 A:HIS378 2.0 25.3 1.0
NE2 A:HIS61 2.0 25.2 1.0
NC A:HEA601 2.1 25.5 1.0
NB A:HEA601 2.1 26.2 1.0
ND A:HEA601 2.1 24.9 1.0
NA A:HEA601 2.1 26.6 1.0
CE1 A:HIS378 2.9 25.7 1.0
CD2 A:HIS61 3.0 25.8 1.0
CE1 A:HIS61 3.0 26.1 1.0
C1B A:HEA601 3.1 26.5 1.0
CD2 A:HIS378 3.1 25.3 1.0
C4C A:HEA601 3.1 25.4 1.0
C4A A:HEA601 3.1 26.9 1.0
C1D A:HEA601 3.1 25.4 1.0
C1A A:HEA601 3.1 25.5 1.0
C1C A:HEA601 3.1 25.4 1.0
C4D A:HEA601 3.1 24.5 1.0
C4B A:HEA601 3.1 26.2 1.0
CHB A:HEA601 3.4 27.2 1.0
CHD A:HEA601 3.4 25.1 1.0
CHC A:HEA601 3.5 25.0 1.0
CHA A:HEA601 3.5 25.1 1.0
ND1 A:HIS378 4.1 25.6 1.0
ND1 A:HIS61 4.2 25.7 1.0
CG A:HIS61 4.2 25.9 1.0
CG A:HIS378 4.2 24.5 1.0
C2A A:HEA601 4.3 26.6 1.0
C3A A:HEA601 4.3 26.0 1.0
C3C A:HEA601 4.3 24.8 1.0
C2B A:HEA601 4.3 26.8 1.0
C3B A:HEA601 4.3 26.9 1.0
C2D A:HEA601 4.3 23.8 1.0
C2C A:HEA601 4.3 25.2 1.0
C3D A:HEA601 4.3 24.3 1.0
OG A:SER382 4.8 29.6 0.5

Iron binding site 2 out of 6 in 5z86

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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 20 Mm Azide Solution For 3 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 20 Mm Azide Solution For 3 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:25.8
occ:0.50
FE A:HEA602 0.0 25.8 0.5
FE A:HEA602 0.9 26.5 0.5
ND A:HEA602 1.5 26.4 0.5
NC A:HEA602 1.8 25.7 0.5
NA A:HEA602 2.1 25.1 0.5
ND A:HEA602 2.1 25.3 0.5
NC A:HEA602 2.1 25.1 0.5
NB A:HEA602 2.1 25.5 0.5
NE2 A:HIS376 2.1 28.3 1.0
N1 A:AZI607 2.2 32.8 1.0
C1D A:HEA602 2.3 26.5 0.5
C4C A:HEA602 2.4 25.9 0.5
NA A:HEA602 2.6 26.6 0.5
CHD A:HEA602 2.7 26.0 0.5
C4D A:HEA602 2.7 26.1 0.5
NB A:HEA602 2.9 26.5 0.5
N2 A:AZI607 3.0 33.9 1.0
C1C A:HEA602 3.0 25.3 0.5
C4D A:HEA602 3.0 24.5 0.5
C1A A:HEA602 3.1 24.9 0.5
C4A A:HEA602 3.1 25.5 0.5
C1C A:HEA602 3.1 24.8 0.5
C4C A:HEA602 3.1 25.0 0.5
C1D A:HEA602 3.1 24.9 0.5
CD2 A:HIS376 3.1 28.1 1.0
C4B A:HEA602 3.1 25.4 0.5
C1B A:HEA602 3.1 25.6 0.5
CE1 A:HIS376 3.1 28.3 1.0
C1A A:HEA602 3.3 26.3 0.5
CHA A:HEA602 3.4 25.6 0.5
CHA A:HEA602 3.4 24.1 0.5
CHC A:HEA602 3.5 24.5 0.5
CHD A:HEA602 3.5 24.6 0.5
CHB A:HEA602 3.5 24.6 0.5
C2D A:HEA602 3.5 26.6 0.5
C4B A:HEA602 3.7 25.6 0.5
C3D A:HEA602 3.7 26.9 0.5
C3C A:HEA602 3.8 25.7 0.5
N1 A:AZI606 3.8 30.8 1.0
C4A A:HEA602 3.8 26.7 0.5
CHC A:HEA602 3.8 25.7 0.5
C1B A:HEA602 3.9 26.2 0.5
C2C A:HEA602 4.0 25.7 0.5
N3 A:AZI607 4.1 33.5 1.0
C3D A:HEA602 4.2 24.4 0.5
C3A A:HEA602 4.3 25.3 0.5
C2A A:HEA602 4.3 25.3 0.5
C2D A:HEA602 4.3 24.5 0.5
ND1 A:HIS376 4.3 28.0 1.0
C3C A:HEA602 4.3 25.1 0.5
C2C A:HEA602 4.3 24.8 0.5
CG A:HIS376 4.3 28.2 1.0
CHB A:HEA602 4.3 26.4 0.5
C3B A:HEA602 4.3 25.4 0.5
C2B A:HEA602 4.3 26.0 0.5
N2 A:AZI606 4.5 32.5 1.0
C2A A:HEA602 4.6 26.0 0.5
CG1 A:VAL380 4.8 24.9 0.5
C3A A:HEA602 4.8 26.2 0.5
CU A:CU603 4.9 28.3 1.0
CMD A:HEA602 4.9 25.7 0.5
C3B A:HEA602 5.0 25.8 0.5
CAC A:HEA602 5.0 25.4 0.5

Iron binding site 3 out of 6 in 5z86

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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 20 Mm Azide Solution For 3 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 20 Mm Azide Solution For 3 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:26.5
occ:0.50
FE A:HEA602 0.0 26.5 0.5
FE A:HEA602 0.9 25.8 0.5
NB A:HEA602 1.5 25.5 0.5
NA A:HEA602 1.7 25.1 0.5
NA A:HEA602 2.1 26.6 0.5
NC A:HEA602 2.1 25.7 0.5
NB A:HEA602 2.1 26.5 0.5
ND A:HEA602 2.1 26.4 0.5
NE2 A:HIS376 2.2 28.3 1.0
N1 A:AZI607 2.2 32.8 1.0
C1B A:HEA602 2.3 25.6 0.5
C4A A:HEA602 2.4 25.5 0.5
CHB A:HEA602 2.7 24.6 0.5
N2 A:AZI607 2.7 33.9 1.0
NC A:HEA602 2.7 25.1 0.5
C4B A:HEA602 2.7 25.4 0.5
ND A:HEA602 2.8 25.3 0.5
C1A A:HEA602 3.0 24.9 0.5
CE1 A:HIS376 3.0 28.3 1.0
C4A A:HEA602 3.1 26.7 0.5
C4C A:HEA602 3.1 25.9 0.5
C1A A:HEA602 3.1 26.3 0.5
C1C A:HEA602 3.1 25.3 0.5
C1B A:HEA602 3.1 26.2 0.5
C4B A:HEA602 3.1 25.6 0.5
C4D A:HEA602 3.1 26.1 0.5
C1D A:HEA602 3.1 26.5 0.5
CD2 A:HIS376 3.2 28.1 1.0
C1C A:HEA602 3.4 24.8 0.5
CHC A:HEA602 3.4 24.5 0.5
CHB A:HEA602 3.5 26.4 0.5
CHD A:HEA602 3.5 26.0 0.5
CHC A:HEA602 3.5 25.7 0.5
CHA A:HEA602 3.5 25.6 0.5
C2B A:HEA602 3.6 26.0 0.5
C4D A:HEA602 3.6 24.5 0.5
N3 A:AZI607 3.6 33.5 1.0
CHA A:HEA602 3.7 24.1 0.5
C3A A:HEA602 3.7 25.3 0.5
C3B A:HEA602 3.7 25.4 0.5
C4C A:HEA602 3.8 25.0 0.5
C1D A:HEA602 3.9 24.9 0.5
C2A A:HEA602 4.0 25.3 0.5
N1 A:AZI606 4.1 30.8 1.0
ND1 A:HIS376 4.2 28.0 1.0
C3A A:HEA602 4.2 26.2 0.5
C2A A:HEA602 4.3 26.0 0.5
C3C A:HEA602 4.3 25.7 0.5
C2C A:HEA602 4.3 25.7 0.5
C2B A:HEA602 4.3 26.6 0.5
CG A:HIS376 4.3 28.2 1.0
C3B A:HEA602 4.3 25.8 0.5
C3D A:HEA602 4.3 26.9 0.5
C2D A:HEA602 4.3 26.6 0.5
CHD A:HEA602 4.3 24.6 0.5
C2C A:HEA602 4.7 24.8 0.5
CA A:GLY355 4.7 29.0 1.0
C3D A:HEA602 4.9 24.4 0.5
CMB A:HEA602 4.9 26.6 0.5
C3C A:HEA602 4.9 25.1 0.5
CU A:CU603 4.9 28.3 1.0
CMA A:HEA602 5.0 26.9 0.5

Iron binding site 4 out of 6 in 5z86

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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 20 Mm Azide Solution For 3 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 20 Mm Azide Solution For 3 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:32.2
occ:1.00
FE N:HEA601 0.0 32.2 1.0
NE2 N:HIS61 2.0 30.6 1.0
NE2 N:HIS378 2.0 30.9 1.0
ND N:HEA601 2.1 30.9 1.0
NA N:HEA601 2.1 32.6 1.0
NB N:HEA601 2.1 32.5 1.0
NC N:HEA601 2.1 31.9 1.0
CE1 N:HIS378 2.9 30.7 1.0
CD2 N:HIS61 3.0 31.7 1.0
CE1 N:HIS61 3.0 31.6 1.0
CD2 N:HIS378 3.0 30.5 1.0
C1B N:HEA601 3.1 33.6 1.0
C4A N:HEA601 3.1 32.9 1.0
C1D N:HEA601 3.1 31.2 1.0
C4C N:HEA601 3.1 31.8 1.0
C1A N:HEA601 3.1 31.3 1.0
C4D N:HEA601 3.1 30.8 1.0
C4B N:HEA601 3.1 33.8 1.0
C1C N:HEA601 3.1 32.1 1.0
CHB N:HEA601 3.4 33.8 1.0
CHD N:HEA601 3.4 31.3 1.0
CHA N:HEA601 3.5 31.3 1.0
CHC N:HEA601 3.5 31.8 1.0
ND1 N:HIS378 4.1 30.6 1.0
ND1 N:HIS61 4.1 31.8 1.0
CG N:HIS61 4.2 31.6 1.0
CG N:HIS378 4.2 30.8 1.0
C2A N:HEA601 4.3 31.7 1.0
C3A N:HEA601 4.3 32.8 1.0
C2B N:HEA601 4.3 33.8 1.0
C2D N:HEA601 4.3 29.8 1.0
C3B N:HEA601 4.3 34.4 1.0
C3D N:HEA601 4.3 29.9 1.0
C3C N:HEA601 4.3 31.6 1.0
C2C N:HEA601 4.3 31.5 1.0
OG N:SER382 4.8 39.2 0.5
CE1 N:PHE377 5.0 32.0 1.0

Iron binding site 5 out of 6 in 5z86

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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 20 Mm Azide Solution For 3 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 20 Mm Azide Solution For 3 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:30.5
occ:0.50
FE N:HEA602 0.0 30.5 0.5
FE N:HEA602 1.0 27.6 0.5
ND N:HEA602 1.4 27.3 0.5
NC N:HEA602 1.7 26.8 0.5
NA N:HEA602 2.1 31.2 0.5
ND N:HEA602 2.1 31.2 0.5
NC N:HEA602 2.1 30.4 0.5
NB N:HEA602 2.1 29.9 0.5
NE2 N:HIS376 2.2 30.5 1.0
C1D N:HEA602 2.2 27.2 0.5
N3 N:AZI607 2.3 36.3 1.0
C4C N:HEA602 2.3 26.9 0.5
CHD N:HEA602 2.5 26.4 0.5
C4D N:HEA602 2.7 27.7 0.5
NA N:HEA602 2.7 28.6 0.5
NB N:HEA602 3.0 27.9 0.5
C1C N:HEA602 3.0 27.0 0.5
C1A N:HEA602 3.1 30.9 0.5
C4C N:HEA602 3.1 30.6 0.5
C4D N:HEA602 3.1 31.3 0.5
C4A N:HEA602 3.1 31.3 0.5
C1C N:HEA602 3.1 30.1 0.5
C1D N:HEA602 3.1 30.8 0.5
N2 N:AZI607 3.1 36.3 1.0
C1B N:HEA602 3.1 30.1 0.5
C4B N:HEA602 3.1 29.4 0.5
CD2 N:HIS376 3.1 30.8 1.0
CE1 N:HIS376 3.2 30.2 1.0
C1A N:HEA602 3.4 28.4 0.5
CHA N:HEA602 3.4 27.6 0.5
CHA N:HEA602 3.5 30.9 0.5
CHD N:HEA602 3.5 30.5 0.5
C2D N:HEA602 3.5 27.4 0.5
CHB N:HEA602 3.5 30.1 0.5
CHC N:HEA602 3.5 29.4 0.5
C3C N:HEA602 3.7 26.8 0.5
C3D N:HEA602 3.7 27.9 0.5
C4B N:HEA602 3.8 27.7 0.5
N1 N:AZI606 3.8 36.2 1.0
CHC N:HEA602 3.8 27.0 0.5
C4A N:HEA602 3.9 28.5 0.5
C2C N:HEA602 4.0 27.1 0.5
C1B N:HEA602 4.1 27.9 0.5
N1 N:AZI607 4.2 35.6 1.0
C3A N:HEA602 4.3 31.6 0.5
C2A N:HEA602 4.3 31.9 0.5
C3C N:HEA602 4.3 30.8 0.5
C2C N:HEA602 4.3 30.3 0.5
C3D N:HEA602 4.3 31.3 0.5
C2D N:HEA602 4.3 31.1 0.5
C3B N:HEA602 4.3 29.4 0.5
C2B N:HEA602 4.3 29.8 0.5
ND1 N:HIS376 4.3 30.4 1.0
CG N:HIS376 4.3 31.0 1.0
CHB N:HEA602 4.4 28.0 0.5
N2 N:AZI606 4.5 37.2 1.0
C2A N:HEA602 4.7 28.6 0.5
CG1 N:VAL380 4.7 32.6 0.5
CMD N:HEA602 4.8 27.5 0.5
CU N:CU603 4.9 32.2 1.0
CAC N:HEA602 4.9 27.0 0.5
C3A N:HEA602 4.9 29.0 0.5
CG2 N:VAL243 5.0 27.4 1.0
CE1 N:HIS240 5.0 28.7 1.0

Iron binding site 6 out of 6 in 5z86

Go back to Iron Binding Sites List in 5z86
Iron binding site 6 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 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 20 Mm Azide Solution For 3 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:27.6
occ:0.50
FE N:HEA602 0.0 27.6 0.5
FE N:HEA602 1.0 30.5 0.5
NB N:HEA602 1.5 29.9 0.5
NA N:HEA602 1.7 31.2 0.5
NA N:HEA602 2.1 28.6 0.5
NC N:HEA602 2.1 26.8 0.5
NB N:HEA602 2.1 27.9 0.5
ND N:HEA602 2.1 27.3 0.5
NE2 N:HIS376 2.2 30.5 1.0
N3 N:AZI607 2.2 36.3 1.0
C1B N:HEA602 2.2 30.1 0.5
C4A N:HEA602 2.3 31.3 0.5
CHB N:HEA602 2.5 30.1 0.5
N2 N:AZI607 2.7 36.3 1.0
C4B N:HEA602 2.7 29.4 0.5
NC N:HEA602 2.8 30.4 0.5
ND N:HEA602 2.9 31.2 0.5
C1A N:HEA602 3.0 30.9 0.5
C4A N:HEA602 3.0 28.5 0.5
C1A N:HEA602 3.0 28.4 0.5
CE1 N:HIS376 3.1 30.2 1.0
C4C N:HEA602 3.1 26.9 0.5
C1C N:HEA602 3.1 27.0 0.5
C4B N:HEA602 3.1 27.7 0.5
C1B N:HEA602 3.1 27.9 0.5
C4D N:HEA602 3.1 27.7 0.5
C1D N:HEA602 3.1 27.2 0.5
CD2 N:HIS376 3.2 30.8 1.0
CHB N:HEA602 3.5 28.0 0.5
C2B N:HEA602 3.5 29.8 0.5
C1C N:HEA602 3.5 30.1 0.5
CHD N:HEA602 3.5 26.4 0.5
CHA N:HEA602 3.5 27.6 0.5
CHC N:HEA602 3.5 29.4 0.5
CHC N:HEA602 3.5 27.0 0.5
N1 N:AZI607 3.6 35.6 1.0
C3A N:HEA602 3.6 31.6 0.5
C3B N:HEA602 3.7 29.4 0.5
C4D N:HEA602 3.7 31.3 0.5
CHA N:HEA602 3.7 30.9 0.5
C4C N:HEA602 3.9 30.6 0.5
C2A N:HEA602 3.9 31.9 0.5
C1D N:HEA602 4.0 30.8 0.5
N1 N:AZI606 4.2 36.2 1.0
ND1 N:HIS376 4.2 30.4 1.0
C3A N:HEA602 4.2 29.0 0.5
C2A N:HEA602 4.2 28.6 0.5
C3C N:HEA602 4.3 26.8 0.5
C2C N:HEA602 4.3 27.1 0.5
C2B N:HEA602 4.3 28.3 0.5
C3B N:HEA602 4.3 28.2 0.5
CG N:HIS376 4.3 31.0 1.0
C3D N:HEA602 4.3 27.9 0.5
C2D N:HEA602 4.3 27.4 0.5
CHD N:HEA602 4.4 30.5 0.5
CA N:GLY355 4.8 33.8 1.0
CMB N:HEA602 4.8 30.2 0.5
C2C N:HEA602 4.8 30.3 0.5
CMA N:HEA602 4.9 32.5 0.5
CU N:CU603 4.9 32.2 1.0
CE1 N:HIS240 4.9 28.7 1.0
C3D N:HEA602 5.0 31.3 0.5

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: Tue Aug 6 13:01:15 2024

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