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Iron in PDB 8gcq: Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution

Enzymatic activity of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution

All present enzymatic activity of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution, PDB code: 8gcq was solved by I.Ishigami, S.-R.Yeh, D.L.Rousseau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.00 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.6, 189.5, 211.1, 90, 90, 90
R / Rfree (%) 23.2 / 26.6

Other elements in 8gcq:

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution (pdb code 8gcq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution, PDB code: 8gcq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8gcq

Go back to Iron Binding Sites List in 8gcq
Iron binding site 1 out of 4 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe605

b:10.9
occ:1.00
 FE A:HEA605 0.0 10.9 1.0
O A:OH607 1.9 9.2 1.0
ND A:HEA605 2.1 11.2 1.0
NA A:HEA605 2.1 10.9 1.0
NC A:HEA605 2.1 11.2 1.0
NB A:HEA605 2.1 12.7 1.0
NE2 A:HIS376 2.2 9.4 1.0
CE1 A:HIS376 2.9 9.1 1.0
C4D A:HEA605 3.0 11.2 1.0
C1A A:HEA605 3.1 10.0 1.0
C4B A:HEA605 3.1 13.4 1.0
C4A A:HEA605 3.1 10.8 1.0
C1C A:HEA605 3.1 11.5 1.0
C4C A:HEA605 3.1 11.1 1.0
C1B A:HEA605 3.2 12.8 1.0
C1D A:HEA605 3.2 11.2 1.0
CHA A:HEA605 3.3 11.1 1.0
CD2 A:HIS376 3.3 9.4 1.0
CHC A:HEA605 3.5 12.7 1.0
CHB A:HEA605 3.5 11.7 1.0
CHD A:HEA605 3.6 11.6 1.0
ND1 A:HIS376 4.1 9.6 1.0
O A:HOH728 4.2 9.2 1.0
CG A:HIS376 4.3 9.4 1.0
C3D A:HEA605 4.4 10.4 1.0
C3A A:HEA605 4.4 9.8 1.0
C2A A:HEA605 4.4 9.2 1.0
C3B A:HEA605 4.4 14.3 1.0
C3C A:HEA605 4.4 11.0 1.0
C2B A:HEA605 4.5 13.0 1.0
C2C A:HEA605 4.5 11.0 1.0
C2D A:HEA605 4.5 10.5 1.0
CU A:CU601 4.7 12.0 1.0
CE1 A:HIS240 5.0 13.6 1.0

Iron binding site 2 out of 4 in 8gcq

Go back to Iron Binding Sites List in 8gcq
Iron binding site 2 out of 4 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe606

b:14.7
occ:1.00
 FE A:HEA606 0.0 14.7 1.0
NE2 A:HIS378 2.0 11.5 1.0
ND A:HEA606 2.1 12.2 1.0
NC A:HEA606 2.1 12.7 1.0
NA A:HEA606 2.1 12.0 1.0
NE2 A:HIS61 2.1 13.0 1.0
NB A:HEA606 2.1 12.0 1.0
CE1 A:HIS378 2.8 10.5 1.0
CD2 A:HIS61 3.0 12.6 1.0
C1D A:HEA606 3.1 12.4 1.0
C4C A:HEA606 3.1 12.8 1.0
C1A A:HEA606 3.1 12.5 1.0
C4A A:HEA606 3.1 12.3 1.0
C4D A:HEA606 3.1 12.5 1.0
C1B A:HEA606 3.1 11.9 1.0
C1C A:HEA606 3.1 12.4 1.0
CE1 A:HIS61 3.2 13.2 1.0
C4B A:HEA606 3.2 12.2 1.0
CD2 A:HIS378 3.2 10.6 1.0
CHD A:HEA606 3.4 11.7 1.0
CHA A:HEA606 3.5 12.7 1.0
CHB A:HEA606 3.5 12.2 1.0
CHC A:HEA606 3.6 11.8 1.0
ND1 A:HIS378 4.0 10.1 1.0
CG A:HIS61 4.2 11.9 1.0
CG A:HIS378 4.2 9.8 1.0
ND1 A:HIS61 4.2 12.2 1.0
C3A A:HEA606 4.3 12.1 1.0
C2D A:HEA606 4.4 11.5 1.0
C2A A:HEA606 4.4 11.8 1.0
C3C A:HEA606 4.4 11.5 1.0
C3D A:HEA606 4.4 12.1 1.0
C2C A:HEA606 4.4 11.3 1.0
C2B A:HEA606 4.5 11.4 1.0
C3B A:HEA606 4.5 11.3 1.0
O A:HOH762 4.9 89.8 1.0

Iron binding site 3 out of 4 in 8gcq

Go back to Iron Binding Sites List in 8gcq
Iron binding site 3 out of 4 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe606

b:19.4
occ:1.00
 FE N:HEA606 0.0 19.4 1.0
NC N:HEA606 2.1 18.5 1.0
NA N:HEA606 2.1 18.4 1.0
ND N:HEA606 2.1 20.0 1.0
NB N:HEA606 2.1 17.5 1.0
O N:OH608 2.2 14.0 1.0
NE2 N:HIS376 2.3 18.1 1.0
C1C N:HEA606 3.0 18.1 1.0
C1A N:HEA606 3.1 20.4 1.0
C4B N:HEA606 3.1 18.1 1.0
C4D N:HEA606 3.1 19.9 1.0
C1B N:HEA606 3.1 16.9 1.0
C4A N:HEA606 3.1 19.6 1.0
C4C N:HEA606 3.1 19.7 1.0
C1D N:HEA606 3.2 20.1 1.0
CD2 N:HIS376 3.3 19.2 1.0
CE1 N:HIS376 3.3 18.9 1.0
CHC N:HEA606 3.4 17.1 1.0
CHA N:HEA606 3.4 21.0 1.0
CHB N:HEA606 3.5 18.5 1.0
CHD N:HEA606 3.5 20.1 1.0
O N:HOH707 4.3 23.0 1.0
C2C N:HEA606 4.4 17.7 1.0
C2A N:HEA606 4.4 19.7 1.0
C2B N:HEA606 4.4 17.3 1.0
C3D N:HEA606 4.4 20.4 1.0
C3A N:HEA606 4.4 21.1 1.0
C3B N:HEA606 4.4 18.6 1.0
ND1 N:HIS376 4.4 20.0 1.0
CG N:HIS376 4.4 20.8 1.0
C3C N:HEA606 4.4 17.4 1.0
C2D N:HEA606 4.5 20.3 1.0
CU N:CU601 4.6 29.6 1.0

Iron binding site 4 out of 4 in 8gcq

Go back to Iron Binding Sites List in 8gcq
Iron binding site 4 out of 4 in the Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Sfx Structure of Oxidized Cytochrome C Oxidase at 2.38 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe607

b:30.1
occ:1.00
 FE N:HEA607 0.0 30.1 1.0
NE2 N:HIS61 1.9 24.2 1.0
NC N:HEA607 2.1 28.3 1.0
NB N:HEA607 2.1 30.0 1.0
NA N:HEA607 2.1 29.2 1.0
ND N:HEA607 2.1 30.1 1.0
NE2 N:HIS378 2.2 31.7 1.0
CE1 N:HIS61 2.8 24.7 1.0
CD2 N:HIS61 2.9 25.1 1.0
C1B N:HEA607 3.0 30.5 1.0
C4A N:HEA607 3.0 27.0 1.0
C4C N:HEA607 3.1 30.9 1.0
CE1 N:HIS378 3.1 32.5 1.0
C1C N:HEA607 3.1 30.3 1.0
C1D N:HEA607 3.1 29.7 1.0
C1A N:HEA607 3.1 29.5 1.0
C4B N:HEA607 3.1 28.8 1.0
C4D N:HEA607 3.2 29.6 1.0
CD2 N:HIS378 3.2 27.9 1.0
CHB N:HEA607 3.4 29.3 1.0
CHD N:HEA607 3.5 29.3 1.0
CHC N:HEA607 3.5 30.2 1.0
CHA N:HEA607 3.5 30.3 1.0
ND1 N:HIS61 3.9 25.5 1.0
CG N:HIS61 4.0 25.4 1.0
ND1 N:HIS378 4.2 32.8 1.0
CG N:HIS378 4.3 29.3 1.0
O N:HOH722 4.3 49.0 1.0
C3A N:HEA607 4.3 27.3 1.0
C2B N:HEA607 4.4 31.5 1.0
C2C N:HEA607 4.4 32.2 1.0
C3C N:HEA607 4.4 29.9 1.0
C2A N:HEA607 4.4 26.3 1.0
C3B N:HEA607 4.4 29.0 1.0
C2D N:HEA607 4.5 29.4 1.0
C3D N:HEA607 4.5 27.7 1.0
O N:HOH763 4.6 72.5 1.0

Reference:

I.Ishigami, R.G.Sierra, Z.Su, A.Peck, C.Wang, F.Poitevin, S.Lisova, B.Hayes, F.R.Moss 3Rd, S.Boutet, R.E.Sublett, C.H.Yoon, S.R.Yeh, D.L.Rousseau. Structural Insights Into Functional Properties of the Oxidized Form of Cytochrome C Oxidase. Nat Commun V. 14 5752 2023.
ISSN: ESSN 2041-1723
PubMed: 37717031
DOI: 10.1038/S41467-023-41533-X
Page generated: Sat Aug 10 04:51:08 2024

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