Atomistry » Iron » PDB 5ych-5zgh » 5zcp
Atomistry »
  Iron »
    PDB 5ych-5zgh »
      5zcp »

Iron in PDB 5zcp: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days

Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days

All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 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 20 Mm Azide Solution For 2 Days, PDB code: 5zcp 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 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.320, 206.171, 177.625, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.7

Other elements in 5zcp:

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

Iron binding site 1 out of 6 in 5zcp

Go back to Iron Binding Sites List in 5zcp
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 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 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:24.6
occ:1.00
FE A:HEA601 0.0 24.6 1.0
NC A:HEA601 2.0 24.4 1.0
NE2 A:HIS378 2.0 21.4 1.0
NE2 A:HIS61 2.0 21.4 1.0
ND A:HEA601 2.0 24.5 1.0
NB A:HEA601 2.0 26.1 1.0
NA A:HEA601 2.0 24.9 1.0
CE1 A:HIS378 2.9 24.6 1.0
CE1 A:HIS61 3.0 24.1 1.0
CD2 A:HIS61 3.0 24.9 1.0
C4D A:HEA601 3.0 22.3 1.0
C1C A:HEA601 3.0 24.0 1.0
C4C A:HEA601 3.0 24.5 1.0
C4A A:HEA601 3.0 24.7 1.0
C4B A:HEA601 3.0 24.0 1.0
C1A A:HEA601 3.0 24.8 1.0
C1B A:HEA601 3.1 21.7 1.0
C1D A:HEA601 3.1 23.6 1.0
CD2 A:HIS378 3.1 25.7 1.0
CHB A:HEA601 3.4 26.2 1.0
CHC A:HEA601 3.4 23.8 1.0
CHA A:HEA601 3.4 23.1 1.0
CHD A:HEA601 3.5 23.6 1.0
ND1 A:HIS378 4.1 25.1 1.0
CG A:HIS61 4.1 22.6 1.0
CG A:HIS378 4.1 22.0 1.0
ND1 A:HIS61 4.1 23.9 1.0
C3A A:HEA601 4.2 23.2 1.0
C2A A:HEA601 4.3 23.8 1.0
C2D A:HEA601 4.3 21.6 1.0
C2C A:HEA601 4.3 23.4 1.0
C3B A:HEA601 4.3 23.8 1.0
C2B A:HEA601 4.3 24.4 1.0
C3C A:HEA601 4.3 22.7 1.0
C3D A:HEA601 4.3 24.1 1.0
OG A:SER382 4.9 27.8 0.5

Iron binding site 2 out of 6 in 5zcp

Go back to Iron Binding Sites List in 5zcp
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 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 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:23.0
occ:0.40
FE A:HEA602 0.0 23.0 0.4
FE A:HEA602 0.9 25.5 0.6
ND A:HEA602 1.4 23.0 0.6
NC A:HEA602 1.7 26.4 0.6
NB A:HEA602 2.0 21.7 0.4
ND A:HEA602 2.1 23.3 0.4
NA A:HEA602 2.1 22.4 0.4
NC A:HEA602 2.1 21.5 0.4
NE2 A:HIS376 2.1 28.6 1.0
N3 A:AZI606 2.2 23.3 0.6
N1 A:AZI607 2.2 24.3 0.4
C1D A:HEA602 2.3 23.9 0.6
C4C A:HEA602 2.4 25.8 0.6
NA A:HEA602 2.6 26.1 0.6
C4D A:HEA602 2.7 22.5 0.6
CHD A:HEA602 2.7 23.4 0.6
NB A:HEA602 2.8 26.0 0.6
C1C A:HEA602 3.0 25.6 0.6
C4B A:HEA602 3.0 22.8 0.4
C4D A:HEA602 3.0 23.3 0.4
C1B A:HEA602 3.1 24.1 0.4
C4C A:HEA602 3.1 21.8 0.4
C1A A:HEA602 3.1 21.0 0.4
CD2 A:HIS376 3.1 27.7 1.0
C1C A:HEA602 3.1 21.4 0.4
C4A A:HEA602 3.1 22.8 0.4
C1D A:HEA602 3.1 22.3 0.4
CE1 A:HIS376 3.2 27.5 1.0
N2 A:AZI607 3.2 27.9 0.4
N2 A:AZI606 3.2 24.0 0.6
C1A A:HEA602 3.3 24.8 0.6
CHA A:HEA602 3.4 22.9 0.6
CHC A:HEA602 3.4 21.3 0.4
CHA A:HEA602 3.4 22.4 0.4
CHB A:HEA602 3.5 22.5 0.4
C2D A:HEA602 3.5 22.4 0.6
CHD A:HEA602 3.5 22.7 0.4
C4B A:HEA602 3.7 24.8 0.6
CHC A:HEA602 3.7 23.9 0.6
C3D A:HEA602 3.7 23.4 0.6
C4A A:HEA602 3.7 26.9 0.6
C3C A:HEA602 3.8 24.4 0.6
C1B A:HEA602 3.9 25.0 0.6
N1 A:AZI607 3.9 24.3 0.6
C2C A:HEA602 4.0 25.6 0.6
C3D A:HEA602 4.2 22.9 0.4
C3B A:HEA602 4.2 21.1 0.4
C3C A:HEA602 4.2 21.6 0.4
CHB A:HEA602 4.3 26.7 0.6
C2D A:HEA602 4.3 23.6 0.4
C2B A:HEA602 4.3 24.3 0.4
C2A A:HEA602 4.3 20.6 0.4
CG A:HIS376 4.3 26.2 1.0
C3A A:HEA602 4.3 21.6 0.4
C2C A:HEA602 4.3 20.8 0.4
ND1 A:HIS376 4.3 26.0 1.0
N3 A:AZI607 4.3 20.2 0.4
N1 A:AZI606 4.4 22.4 0.6
N2 A:AZI607 4.5 29.3 0.6
CG1 A:VAL380 4.6 24.8 0.5
C2A A:HEA602 4.6 23.5 0.6
C3A A:HEA602 4.8 24.4 0.6
CMD A:HEA602 4.8 21.1 0.6
CU A:CU603 4.9 26.8 1.0
C3B A:HEA602 5.0 25.1 0.6
CAC A:HEA602 5.0 25.9 0.6

Iron binding site 3 out of 6 in 5zcp

Go back to Iron Binding Sites List in 5zcp
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 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 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:25.5
occ:0.60
FE A:HEA602 0.0 25.5 0.6
FE A:HEA602 0.9 23.0 0.4
NB A:HEA602 1.4 21.7 0.4
NA A:HEA602 1.7 22.4 0.4
N3 A:AZI606 2.0 23.3 0.6
NA A:HEA602 2.0 26.1 0.6
NB A:HEA602 2.0 26.0 0.6
NC A:HEA602 2.1 26.4 0.6
ND A:HEA602 2.1 23.0 0.6
NE2 A:HIS376 2.1 28.6 1.0
C1B A:HEA602 2.2 24.1 0.4
C4A A:HEA602 2.4 22.8 0.4
N1 A:AZI607 2.4 24.3 0.4
CHB A:HEA602 2.7 22.5 0.4
C4B A:HEA602 2.7 22.8 0.4
NC A:HEA602 2.7 21.5 0.4
N2 A:AZI606 2.8 24.0 0.6
ND A:HEA602 2.8 23.3 0.4
C1A A:HEA602 2.9 21.0 0.4
C4A A:HEA602 3.0 26.9 0.6
C1A A:HEA602 3.0 24.8 0.6
CE1 A:HIS376 3.0 27.5 1.0
C4D A:HEA602 3.0 22.5 0.6
C1C A:HEA602 3.1 25.6 0.6
C1B A:HEA602 3.1 25.0 0.6
C4B A:HEA602 3.1 24.8 0.6
C4C A:HEA602 3.1 25.8 0.6
C1D A:HEA602 3.1 23.9 0.6
CD2 A:HIS376 3.1 27.7 1.0
CHB A:HEA602 3.4 26.7 0.6
CHC A:HEA602 3.4 21.3 0.4
CHA A:HEA602 3.4 22.9 0.6
CHC A:HEA602 3.4 23.9 0.6
C1C A:HEA602 3.5 21.4 0.4
CHD A:HEA602 3.5 23.4 0.6
C2B A:HEA602 3.5 24.3 0.4
C4D A:HEA602 3.5 23.3 0.4
N2 A:AZI607 3.6 27.9 0.4
CHA A:HEA602 3.6 22.4 0.4
C3B A:HEA602 3.7 21.1 0.4
C3A A:HEA602 3.7 21.6 0.4
N1 A:AZI606 3.8 22.4 0.6
C4C A:HEA602 3.8 21.8 0.4
C1D A:HEA602 4.0 22.3 0.4
C2A A:HEA602 4.0 20.6 0.4
N1 A:AZI607 4.1 24.3 0.6
C3A A:HEA602 4.2 24.4 0.6
C2A A:HEA602 4.2 23.5 0.6
ND1 A:HIS376 4.2 26.0 1.0
C2C A:HEA602 4.3 25.6 0.6
C3D A:HEA602 4.3 23.4 0.6
CG A:HIS376 4.3 26.2 1.0
C2B A:HEA602 4.3 25.6 0.6
C3B A:HEA602 4.3 25.1 0.6
C2D A:HEA602 4.3 22.4 0.6
C3C A:HEA602 4.3 24.4 0.6
CHD A:HEA602 4.4 22.7 0.4
CA A:GLY355 4.8 28.1 1.0
N3 A:AZI607 4.8 20.2 0.4
C2C A:HEA602 4.8 20.8 0.4
C3D A:HEA602 4.8 22.9 0.4
N2 A:AZI607 4.9 29.3 0.6
C3C A:HEA602 4.9 21.6 0.4
CMB A:HEA602 4.9 24.1 0.4
CU A:CU603 5.0 26.8 1.0
CG1 A:VAL380 5.0 24.8 0.5

Iron binding site 4 out of 6 in 5zcp

Go back to Iron Binding Sites List in 5zcp
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 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 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:29.6
occ:1.00
FE N:HEA602 0.0 29.6 1.0
NE2 N:HIS61 1.9 26.1 1.0
NC N:HEA602 2.0 28.6 1.0
NA N:HEA602 2.0 31.4 1.0
NB N:HEA602 2.0 30.1 1.0
ND N:HEA602 2.0 30.8 1.0
NE2 N:HIS378 2.0 26.7 1.0
CE1 N:HIS378 2.9 27.7 1.0
CE1 N:HIS61 2.9 31.0 1.0
CD2 N:HIS61 3.0 31.9 1.0
C4B N:HEA602 3.0 28.8 1.0
C4A N:HEA602 3.0 30.1 1.0
C1A N:HEA602 3.0 30.1 1.0
C4D N:HEA602 3.0 28.3 1.0
C1C N:HEA602 3.0 29.3 1.0
C1D N:HEA602 3.0 31.9 1.0
C4C N:HEA602 3.0 29.4 1.0
C1B N:HEA602 3.0 31.6 1.0
CD2 N:HIS378 3.1 29.1 1.0
CHB N:HEA602 3.4 32.8 1.0
CHC N:HEA602 3.4 28.0 1.0
CHA N:HEA602 3.4 29.9 1.0
CHD N:HEA602 3.5 30.3 1.0
ND1 N:HIS378 4.1 29.0 1.0
ND1 N:HIS61 4.1 28.9 1.0
CG N:HIS61 4.1 28.1 1.0
CG N:HIS378 4.2 26.2 1.0
C3A N:HEA602 4.2 29.8 1.0
C2A N:HEA602 4.2 29.1 1.0
C3B N:HEA602 4.2 28.9 1.0
C2B N:HEA602 4.2 29.6 1.0
C2D N:HEA602 4.2 27.7 1.0
C3D N:HEA602 4.3 27.8 1.0
C3C N:HEA602 4.3 28.7 1.0
C2C N:HEA602 4.3 27.4 1.0
OG N:SER382 4.9 40.4 0.5
CE1 N:PHE377 5.0 29.8 1.0

Iron binding site 5 out of 6 in 5zcp

Go back to Iron Binding Sites List in 5zcp
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 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 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:24.6
occ:0.40
FE N:HEA603 0.0 24.6 0.4
FE N:HEA603 0.9 28.8 0.6
ND N:HEA603 1.4 27.4 0.6
NC N:HEA603 1.5 25.8 0.6
N1 N:AZI608 1.9 40.0 0.4
NB N:HEA603 2.0 22.4 0.4
NA N:HEA603 2.0 25.1 0.4
ND N:HEA603 2.1 23.9 0.4
NC N:HEA603 2.1 24.6 0.4
C1D N:HEA603 2.1 25.8 0.6
NE2 N:HIS376 2.2 30.9 1.0
N3 N:AZI607 2.2 28.7 0.6
N2 N:AZI608 2.3 29.1 0.4
C4C N:HEA603 2.3 28.6 0.6
CHD N:HEA603 2.5 24.8 0.6
C4D N:HEA603 2.7 27.1 0.6
NA N:HEA603 2.7 29.4 0.6
C1C N:HEA603 2.8 28.0 0.6
NB N:HEA603 2.8 30.6 0.6
C1B N:HEA603 3.0 25.9 0.4
C4A N:HEA603 3.0 24.2 0.4
C1A N:HEA603 3.0 23.0 0.4
C4B N:HEA603 3.0 22.2 0.4
C4D N:HEA603 3.0 24.6 0.4
C4C N:HEA603 3.1 22.9 0.4
C1D N:HEA603 3.1 23.5 0.4
C1C N:HEA603 3.1 24.0 0.4
CD2 N:HIS376 3.1 31.4 1.0
N2 N:AZI607 3.2 27.5 0.6
N3 N:AZI608 3.2 38.2 0.4
CE1 N:HIS376 3.2 32.0 1.0
C1A N:HEA603 3.4 27.1 0.6
CHA N:HEA603 3.4 25.6 0.6
CHB N:HEA603 3.4 24.2 0.4
CHA N:HEA603 3.4 23.0 0.4
CHD N:HEA603 3.5 23.2 0.4
C2D N:HEA603 3.5 26.3 0.6
CHC N:HEA603 3.5 21.6 0.4
C3C N:HEA603 3.6 27.4 0.6
C4B N:HEA603 3.6 30.2 0.6
CHC N:HEA603 3.7 28.6 0.6
C3D N:HEA603 3.7 29.1 0.6
C2C N:HEA603 3.8 31.7 0.6
C4A N:HEA603 3.9 28.7 0.6
C1B N:HEA603 4.0 29.1 0.6
N1 N:AZI608 4.1 26.3 0.6
C2D N:HEA603 4.2 25.7 0.4
C2B N:HEA603 4.2 25.9 0.4
C3C N:HEA603 4.3 24.3 0.4
C3A N:HEA603 4.3 25.6 0.4
C3B N:HEA603 4.3 24.4 0.4
C2A N:HEA603 4.3 25.8 0.4
C3D N:HEA603 4.3 23.9 0.4
C2C N:HEA603 4.3 23.4 0.4
N1 N:AZI607 4.3 23.5 0.6
CG N:HIS376 4.3 29.7 1.0
ND1 N:HIS376 4.3 29.7 1.0
CHB N:HEA603 4.4 27.2 0.6
CG1 N:VAL380 4.4 29.6 0.5
N2 N:AZI608 4.7 24.9 0.6
C2A N:HEA603 4.7 28.6 0.6
CMD N:HEA603 4.9 28.1 0.6
CAC N:HEA603 4.9 32.3 0.6
CU N:CU604 4.9 30.1 1.0
C3A N:HEA603 4.9 30.5 0.6
C3B N:HEA603 5.0 29.4 0.6

Iron binding site 6 out of 6 in 5zcp

Go back to Iron Binding Sites List in 5zcp
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 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 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:28.8
occ:0.60
FE N:HEA603 0.0 28.8 0.6
FE N:HEA603 0.9 24.6 0.4
NB N:HEA603 1.4 22.4 0.4
NA N:HEA603 1.6 25.1 0.4
NC N:HEA603 1.9 25.8 0.6
N1 N:AZI608 1.9 40.0 0.4
N3 N:AZI607 2.0 28.7 0.6
ND N:HEA603 2.0 27.4 0.6
NA N:HEA603 2.0 29.4 0.6
NB N:HEA603 2.0 30.6 0.6
NE2 N:HIS376 2.1 30.9 1.0
C1B N:HEA603 2.1 25.9 0.4
C4A N:HEA603 2.3 24.2 0.4
CHB N:HEA603 2.5 24.2 0.4
N2 N:AZI608 2.5 29.1 0.4
N2 N:AZI607 2.7 27.5 0.6
C4B N:HEA603 2.7 22.2 0.4
NC N:HEA603 2.8 24.6 0.4
ND N:HEA603 2.9 23.9 0.4
C1A N:HEA603 2.9 23.0 0.4
C1C N:HEA603 2.9 28.0 0.6
C1A N:HEA603 3.0 27.1 0.6
C4C N:HEA603 3.0 28.6 0.6
C4A N:HEA603 3.0 28.7 0.6
C1D N:HEA603 3.0 25.8 0.6
C4B N:HEA603 3.0 30.2 0.6
C4D N:HEA603 3.1 27.1 0.6
C1B N:HEA603 3.1 29.1 0.6
CE1 N:HIS376 3.1 32.0 1.0
CD2 N:HIS376 3.2 31.4 1.0
CHA N:HEA603 3.4 25.6 0.6
CHC N:HEA603 3.4 28.6 0.6
CHD N:HEA603 3.4 24.8 0.6
CHB N:HEA603 3.5 27.2 0.6
C2B N:HEA603 3.5 25.9 0.4
C1C N:HEA603 3.5 24.0 0.4
CHC N:HEA603 3.5 21.6 0.4
N3 N:AZI608 3.6 38.2 0.4
C3A N:HEA603 3.6 25.6 0.4
C4D N:HEA603 3.6 24.6 0.4
CHA N:HEA603 3.7 23.0 0.4
C3B N:HEA603 3.7 24.4 0.4
N1 N:AZI607 3.7 23.5 0.6
C2A N:HEA603 3.9 25.8 0.4
C4C N:HEA603 3.9 22.9 0.4
C1D N:HEA603 4.0 23.5 0.4
C2C N:HEA603 4.2 31.7 0.6
C3C N:HEA603 4.2 27.4 0.6
C3A N:HEA603 4.2 30.5 0.6
C2A N:HEA603 4.2 28.6 0.6
C3B N:HEA603 4.3 29.4 0.6
ND1 N:HIS376 4.3 29.7 1.0
C2B N:HEA603 4.3 30.5 0.6
C2D N:HEA603 4.3 26.3 0.6
C3D N:HEA603 4.3 29.1 0.6
CG N:HIS376 4.3 29.7 1.0
CHD N:HEA603 4.4 23.2 0.4
N1 N:AZI608 4.4 26.3 0.6
CA N:GLY355 4.7 32.7 1.0
CMB N:HEA603 4.8 27.1 0.4
C2C N:HEA603 4.8 23.4 0.4
CMA N:HEA603 4.9 25.9 0.4
CU N:CU604 4.9 30.1 1.0
CG1 N:VAL380 4.9 29.6 0.5
C3D N:HEA603 4.9 23.9 0.4
C3C N:HEA603 5.0 24.3 0.4
CE1 N:HIS240 5.0 25.9 1.0

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 16:19:15 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy