Iron in PDB 8gvm: The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days

Enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days

All present enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days:
7.1.1.9;

Protein crystallography data

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days, PDB code: 8gvm was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.97 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.405, 206.272, 177.609, 90, 90, 90
R / Rfree (%) 16.4 / 18.8

Other elements in 8gvm:

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days (pdb code 8gvm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days, PDB code: 8gvm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8gvm

Go back to Iron Binding Sites List in 8gvm
Iron binding site 1 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:26.2
occ:1.00
FE A:HEA601 0.0 26.2 1.0
NE2 A:HIS61 2.0 23.9 1.0
NE2 A:HIS378 2.0 26.2 1.0
NB A:HEA601 2.0 26.5 1.0
NC A:HEA601 2.0 28.7 1.0
ND A:HEA601 2.0 24.0 1.0
NA A:HEA601 2.0 28.6 1.0
CE1 A:HIS378 2.9 31.1 1.0
CE1 A:HIS61 3.0 30.3 1.0
CD2 A:HIS61 3.0 27.5 1.0
C1A A:HEA601 3.0 28.5 1.0
C4A A:HEA601 3.0 26.7 1.0
C4C A:HEA601 3.0 26.7 1.0
C1C A:HEA601 3.0 28.3 1.0
C1D A:HEA601 3.1 26.9 1.0
C4D A:HEA601 3.1 25.3 1.0
C1B A:HEA601 3.1 24.9 1.0
CD2 A:HIS378 3.1 26.9 1.0
C4B A:HEA601 3.1 25.2 1.0
CHA A:HEA601 3.4 24.9 1.0
CHC A:HEA601 3.4 22.0 1.0
CHB A:HEA601 3.5 28.6 1.0
CHD A:HEA601 3.5 24.2 1.0
ND1 A:HIS378 4.1 26.2 1.0
ND1 A:HIS61 4.1 26.8 1.0
CG A:HIS61 4.1 25.7 1.0
CG A:HIS378 4.2 24.4 1.0
C3A A:HEA601 4.2 23.7 1.0
C2A A:HEA601 4.2 26.9 1.0
C2C A:HEA601 4.3 24.5 1.0
C3B A:HEA601 4.3 27.4 1.0
C2D A:HEA601 4.3 25.7 1.0
C3C A:HEA601 4.3 24.5 1.0
C2B A:HEA601 4.3 27.2 1.0
C3D A:HEA601 4.3 28.9 1.0
OG A:SER382 4.7 37.8 0.5

Iron binding site 2 out of 6 in 8gvm

Go back to Iron Binding Sites List in 8gvm
Iron binding site 2 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:25.9
occ:0.50
FE A:HEA602 0.0 25.9 0.5
FE A:HEA602 0.9 26.5 0.5
ND A:HEA602 1.3 22.0 0.5
NC A:HEA602 1.8 29.4 0.5
NE2 A:HIS376 2.0 29.3 1.0
NB A:HEA602 2.0 24.9 0.5
ND A:HEA602 2.0 30.6 0.5
NA A:HEA602 2.0 26.5 0.5
NC A:HEA602 2.0 20.4 0.5
N1 A:AZI607 2.2 34.5 0.8
C1D A:HEA602 2.3 21.6 0.5
C4C A:HEA602 2.5 34.0 0.5
NA A:HEA602 2.5 31.3 0.5
C4D A:HEA602 2.6 20.9 0.5
N1 A:AZI607 2.6 42.5 0.1
CHD A:HEA602 2.8 19.3 0.5
NB A:HEA602 2.8 37.1 0.5
CD2 A:HIS376 3.0 29.0 1.0
C4D A:HEA602 3.0 27.1 0.5
C4B A:HEA602 3.0 35.6 0.5
N2 A:AZI607 3.0 21.6 0.1
N2 A:AZI607 3.0 30.1 0.8
C1C A:HEA602 3.0 31.5 0.5
C1A A:HEA602 3.0 25.9 0.5
CE1 A:HIS376 3.1 30.0 1.0
C1B A:HEA602 3.1 18.3 0.5
C1C A:HEA602 3.1 32.7 0.5
C4A A:HEA602 3.1 20.2 0.5
C1D A:HEA602 3.1 25.2 0.5
C4C A:HEA602 3.1 28.4 0.5
C1A A:HEA602 3.3 33.6 0.5
CHA A:HEA602 3.3 17.8 0.5
CHC A:HEA602 3.4 17.0 0.5
CHA A:HEA602 3.4 32.4 0.5
CHB A:HEA602 3.5 28.7 0.5
C2D A:HEA602 3.5 26.2 0.5
CHD A:HEA602 3.6 23.0 0.5
C4B A:HEA602 3.7 31.7 0.5
C3D A:HEA602 3.7 25.1 0.5
C4A A:HEA602 3.7 33.9 0.5
CHC A:HEA602 3.8 24.8 0.5
N3 A:AZI607 3.8 29.1 0.1
C3C A:HEA602 3.8 21.9 0.5
C1B A:HEA602 3.9 32.0 0.5
C2C A:HEA602 4.1 26.8 0.5
CG A:HIS376 4.1 32.1 1.0
ND1 A:HIS376 4.2 28.5 1.0
N3 A:AZI607 4.2 32.0 0.8
N1 A:AZI606 4.2 27.5 0.8
C3D A:HEA602 4.2 27.9 0.5
C3B A:HEA602 4.2 22.8 0.5
CHB A:HEA602 4.2 22.7 0.5
C2B A:HEA602 4.2 35.9 0.5
C3A A:HEA602 4.2 34.8 0.5
C2A A:HEA602 4.2 26.8 0.5
C2D A:HEA602 4.3 22.2 0.5
C3C A:HEA602 4.3 27.6 0.5
C2C A:HEA602 4.3 34.8 0.5
CG1 A:VAL380 4.6 20.1 0.5
C2A A:HEA602 4.6 20.7 0.5
N2 A:AZI606 4.7 30.8 0.8
C3A A:HEA602 4.8 18.1 0.5
CMD A:HEA602 4.9 19.8 0.5
CU A:CU603 5.0 28.7 1.0
C3B A:HEA602 5.0 27.7 0.5

Iron binding site 3 out of 6 in 8gvm

Go back to Iron Binding Sites List in 8gvm
Iron binding site 3 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 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 25.9 0.5
NB A:HEA602 1.3 24.9 0.5
NA A:HEA602 1.7 26.5 0.5
NA A:HEA602 2.0 31.3 0.5
NB A:HEA602 2.0 37.1 0.5
NC A:HEA602 2.0 29.4 0.5
ND A:HEA602 2.0 22.0 0.5
NE2 A:HIS376 2.1 29.3 1.0
N1 A:AZI607 2.1 34.5 0.8
C1B A:HEA602 2.2 18.3 0.5
C4A A:HEA602 2.4 20.2 0.5
N1 A:AZI607 2.5 42.5 0.1
N2 A:AZI607 2.6 30.1 0.8
C4B A:HEA602 2.6 35.6 0.5
NC A:HEA602 2.6 20.4 0.5
CHB A:HEA602 2.7 28.7 0.5
ND A:HEA602 2.8 30.6 0.5
C1A A:HEA602 3.0 25.9 0.5
C4A A:HEA602 3.0 33.9 0.5
CE1 A:HIS376 3.0 30.0 1.0
C1B A:HEA602 3.0 32.0 0.5
C1C A:HEA602 3.0 31.5 0.5
C1A A:HEA602 3.0 33.6 0.5
C4B A:HEA602 3.0 31.7 0.5
C4D A:HEA602 3.0 20.9 0.5
C4C A:HEA602 3.1 34.0 0.5
C1D A:HEA602 3.1 21.6 0.5
CD2 A:HIS376 3.1 29.0 1.0
N2 A:AZI607 3.2 21.6 0.1
CHC A:HEA602 3.3 17.0 0.5
CHB A:HEA602 3.4 22.7 0.5
C1C A:HEA602 3.4 32.7 0.5
CHC A:HEA602 3.4 24.8 0.5
CHA A:HEA602 3.4 17.8 0.5
C2B A:HEA602 3.5 35.9 0.5
N3 A:AZI607 3.6 32.0 0.8
CHD A:HEA602 3.6 19.3 0.5
C4D A:HEA602 3.6 27.1 0.5
C3B A:HEA602 3.6 22.8 0.5
C3A A:HEA602 3.7 34.8 0.5
CHA A:HEA602 3.7 32.4 0.5
C4C A:HEA602 3.8 28.4 0.5
C1D A:HEA602 3.9 25.2 0.5
C2A A:HEA602 4.0 26.8 0.5
ND1 A:HIS376 4.2 28.5 1.0
C3A A:HEA602 4.2 18.1 0.5
N3 A:AZI607 4.2 29.1 0.1
C2A A:HEA602 4.2 20.7 0.5
C2B A:HEA602 4.2 32.8 0.5
CG A:HIS376 4.2 32.1 1.0
C3B A:HEA602 4.3 27.7 0.5
C2C A:HEA602 4.3 26.8 0.5
C3C A:HEA602 4.3 21.9 0.5
C3D A:HEA602 4.3 25.1 0.5
C2D A:HEA602 4.3 26.2 0.5
CHD A:HEA602 4.4 23.0 0.5
N1 A:AZI606 4.5 27.5 0.8
C2C A:HEA602 4.7 34.8 0.5
CA A:GLY355 4.8 28.1 1.0
CMB A:HEA602 4.8 29.7 0.5
C3D A:HEA602 4.9 27.9 0.5
C3C A:HEA602 4.9 27.6 0.5
CU A:CU603 4.9 28.7 1.0
CMA A:HEA602 5.0 51.5 0.5

Iron binding site 4 out of 6 in 8gvm

Go back to Iron Binding Sites List in 8gvm
Iron binding site 4 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:32.2
occ:1.00
FE N:HEA602 0.0 32.2 1.0
NE2 N:HIS61 2.0 29.5 1.0
NC N:HEA602 2.0 31.7 1.0
NE2 N:HIS378 2.0 34.6 1.0
NA N:HEA602 2.0 35.7 1.0
ND N:HEA602 2.0 30.1 1.0
NB N:HEA602 2.0 32.9 1.0
CE1 N:HIS378 2.9 35.8 1.0
CE1 N:HIS61 3.0 35.9 1.0
CD2 N:HIS61 3.0 31.8 1.0
C1A N:HEA602 3.0 32.8 1.0
C1D N:HEA602 3.0 31.3 1.0
C4A N:HEA602 3.0 33.2 1.0
C4C N:HEA602 3.0 38.2 1.0
C1B N:HEA602 3.0 32.4 1.0
C1C N:HEA602 3.0 35.4 1.0
C4B N:HEA602 3.1 34.0 1.0
CD2 N:HIS378 3.1 31.2 1.0
C4D N:HEA602 3.1 31.7 1.0
CHB N:HEA602 3.4 31.8 1.0
CHD N:HEA602 3.4 29.8 1.0
CHA N:HEA602 3.5 32.8 1.0
CHC N:HEA602 3.5 29.8 1.0
ND1 N:HIS378 4.1 34.8 1.0
ND1 N:HIS61 4.1 30.8 1.0
CG N:HIS61 4.1 33.7 1.0
CG N:HIS378 4.2 35.4 1.0
C2A N:HEA602 4.2 32.0 1.0
C3A N:HEA602 4.2 33.0 1.0
C3C N:HEA602 4.2 36.1 1.0
C3B N:HEA602 4.3 34.4 1.0
C2D N:HEA602 4.3 32.0 1.0
C2C N:HEA602 4.3 30.2 1.0
C2B N:HEA602 4.3 35.8 1.0
C3D N:HEA602 4.3 27.7 1.0
OG N:SER382 4.9 53.8 0.5
CE1 N:PHE377 4.9 35.4 1.0

Iron binding site 5 out of 6 in 8gvm

Go back to Iron Binding Sites List in 8gvm
Iron binding site 5 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:27.5
occ:0.50
FE N:HEA603 0.0 27.5 0.5
FE N:HEA603 1.0 30.2 0.5
ND N:HEA603 1.5 26.3 0.5
NC N:HEA603 1.6 27.8 0.5
NC N:HEA603 2.0 25.1 0.5
ND N:HEA603 2.0 40.1 0.5
NA N:HEA603 2.0 30.3 0.5
NB N:HEA603 2.0 21.4 0.5
NE2 N:HIS376 2.0 35.3 1.0
C1D N:HEA603 2.2 19.4 0.5
N1 N:AZI608 2.2 40.9 0.9
C4C N:HEA603 2.2 41.5 0.5
CHD N:HEA603 2.4 19.6 0.5
N3 N:AZI608 2.5 39.1 0.1
C4D N:HEA603 2.7 31.0 0.5
NA N:HEA603 2.7 32.8 0.5
NB N:HEA603 2.9 43.5 0.5
C1C N:HEA603 2.9 37.1 0.5
N2 N:AZI608 2.9 42.4 0.9
C4D N:HEA603 3.0 26.5 0.5
C1C N:HEA603 3.0 31.3 0.5
C1A N:HEA603 3.0 24.0 0.5
CE1 N:HIS376 3.0 33.0 1.0
C1B N:HEA603 3.0 16.5 0.5
C4B N:HEA603 3.0 21.8 0.5
C4A N:HEA603 3.0 29.1 0.5
C4C N:HEA603 3.0 24.4 0.5
CD2 N:HIS376 3.1 35.0 1.0
N2 N:AZI608 3.1 29.6 0.1
C1D N:HEA603 3.1 27.1 0.5
CHA N:HEA603 3.4 23.5 0.5
C1A N:HEA603 3.4 35.6 0.5
CHC N:HEA603 3.4 18.6 0.5
CHB N:HEA603 3.5 27.4 0.5
CHA N:HEA603 3.5 25.4 0.5
C2D N:HEA603 3.5 30.5 0.5
CHD N:HEA603 3.5 23.8 0.5
C3C N:HEA603 3.6 23.1 0.5
C4B N:HEA603 3.7 31.2 0.5
C3D N:HEA603 3.8 31.2 0.5
CHC N:HEA603 3.8 31.9 0.5
C2C N:HEA603 3.9 34.7 0.5
C4A N:HEA603 3.9 36.3 0.5
N3 N:AZI608 4.0 38.7 0.9
N1 N:AZI608 4.0 38.8 0.1
C1B N:HEA603 4.0 31.8 0.5
N1 N:AZI607 4.1 34.8 0.9
ND1 N:HIS376 4.2 33.4 1.0
CG N:HIS376 4.2 32.6 1.0
C3D N:HEA603 4.2 22.2 0.5
C3C N:HEA603 4.2 35.5 0.5
C2C N:HEA603 4.2 26.7 0.5
C3A N:HEA603 4.2 30.1 0.5
C2A N:HEA603 4.2 32.2 0.5
C3B N:HEA603 4.2 29.0 0.5
C2B N:HEA603 4.3 27.6 0.5
C2D N:HEA603 4.3 23.2 0.5
CHB N:HEA603 4.4 26.3 0.5
CG1 N:VAL380 4.6 28.8 0.5
CMD N:HEA603 4.7 33.2 0.5
N2 N:AZI607 4.7 39.4 0.9
C2A N:HEA603 4.8 28.1 0.5
CAC N:HEA603 4.8 27.4 0.5
CU N:CU604 4.9 31.4 1.0
C3A N:HEA603 5.0 32.6 0.5

Iron binding site 6 out of 6 in 8gvm

Go back to Iron Binding Sites List in 8gvm
Iron binding site 6 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Crystals Exposed to 20 Mm Azide Solution For 4 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:30.2
occ:0.50
FE N:HEA603 0.0 30.2 0.5
FE N:HEA603 1.0 27.5 0.5
NB N:HEA603 1.4 21.4 0.5
NA N:HEA603 1.6 30.3 0.5
NC N:HEA603 2.0 27.8 0.5
NA N:HEA603 2.0 32.8 0.5
NB N:HEA603 2.0 43.5 0.5
NE2 N:HIS376 2.1 35.3 1.0
ND N:HEA603 2.1 26.3 0.5
C1B N:HEA603 2.1 16.5 0.5
C4A N:HEA603 2.2 29.1 0.5
N1 N:AZI608 2.2 40.9 0.9
CHB N:HEA603 2.5 27.4 0.5
N3 N:AZI608 2.5 39.1 0.1
N2 N:AZI608 2.6 42.4 0.9
C4B N:HEA603 2.7 21.8 0.5
NC N:HEA603 2.8 25.1 0.5
C1A N:HEA603 2.9 24.0 0.5
ND N:HEA603 2.9 40.1 0.5
CE1 N:HIS376 3.0 33.0 1.0
C4A N:HEA603 3.0 36.3 0.5
C1A N:HEA603 3.0 35.6 0.5
C4C N:HEA603 3.0 41.5 0.5
C1C N:HEA603 3.0 37.1 0.5
C1B N:HEA603 3.1 31.8 0.5
C4B N:HEA603 3.1 31.2 0.5
C1D N:HEA603 3.1 19.4 0.5
CD2 N:HIS376 3.1 35.0 1.0
C4D N:HEA603 3.1 31.0 0.5
CHB N:HEA603 3.4 26.3 0.5
CHD N:HEA603 3.4 19.6 0.5
N2 N:AZI608 3.4 29.6 0.1
C2B N:HEA603 3.4 27.6 0.5
N3 N:AZI608 3.4 38.7 0.9
CHA N:HEA603 3.5 25.4 0.5
C1C N:HEA603 3.5 31.3 0.5
CHC N:HEA603 3.5 31.9 0.5
CHC N:HEA603 3.5 18.6 0.5
C3A N:HEA603 3.5 30.1 0.5
C4D N:HEA603 3.6 26.5 0.5
CHA N:HEA603 3.6 23.5 0.5
C3B N:HEA603 3.7 29.0 0.5
C2A N:HEA603 3.8 32.2 0.5
C4C N:HEA603 4.0 24.4 0.5
C1D N:HEA603 4.1 27.1 0.5
ND1 N:HIS376 4.1 33.4 1.0
C3A N:HEA603 4.2 32.6 0.5
CG N:HIS376 4.2 32.6 1.0
C2A N:HEA603 4.2 28.1 0.5
C3C N:HEA603 4.2 23.1 0.5
C2C N:HEA603 4.2 34.7 0.5
C2B N:HEA603 4.3 41.3 0.5
C3B N:HEA603 4.3 29.9 0.5
C2D N:HEA603 4.3 30.5 0.5
C3D N:HEA603 4.4 31.2 0.5
N1 N:AZI607 4.5 34.8 0.9
N1 N:AZI608 4.5 38.8 0.1
CHD N:HEA603 4.5 23.8 0.5
CA N:GLY355 4.7 37.2 1.0
CMB N:HEA603 4.7 25.0 0.5
CMA N:HEA603 4.8 38.3 0.5
C2C N:HEA603 4.8 26.7 0.5
C3D N:HEA603 4.9 22.2 0.5
CU N:CU604 5.0 31.4 1.0

Reference:

A.Shimada, K.Hatano, H.Tadehara, N.Yano, K.Sinzawa-Itoh, E.Yamashita, K.Mutamoto, 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 ESSN 1083-351X
PubMed: 30077971
DOI: 10.1074/JBC.RA118.003123
Page generated: Wed Apr 5 08:59:14 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy