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Iron in PDB 5iy5: Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution

Enzymatic activity of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution

All present enzymatic activity of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution, PDB code: 5iy5 was solved by S.Shimada, J.Baba, S.Aoe, A.Shimada, E.Yamashita, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.290, 183.872, 148.929, 90.00, 102.12, 90.00
R / Rfree (%) 16.7 / 20.7

Other elements in 5iy5:

The structure of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution (pdb code 5iy5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution, PDB code: 5iy5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5iy5

Go back to Iron Binding Sites List in 5iy5
Iron binding site 1 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:27.0
occ:1.00
FE A:HEA604 0.0 27.0 1.0
NE2 A:HIS61 1.9 19.6 1.0
NE2 A:HIS378 1.9 17.1 1.0
NC A:HEA604 2.0 29.9 1.0
NB A:HEA604 2.0 31.8 1.0
NA A:HEA604 2.0 30.7 1.0
ND A:HEA604 2.0 32.5 1.0
CD2 A:HIS61 2.8 23.0 1.0
CD2 A:HIS378 2.9 19.6 1.0
CE1 A:HIS61 2.9 24.7 1.0
CE1 A:HIS378 3.0 23.7 1.0
C1B A:HEA604 3.0 27.7 1.0
C4C A:HEA604 3.0 27.9 1.0
C4A A:HEA604 3.0 27.4 1.0
C1D A:HEA604 3.0 27.5 1.0
C1A A:HEA604 3.0 28.6 1.0
C4D A:HEA604 3.0 30.3 1.0
C1C A:HEA604 3.1 27.8 1.0
C4B A:HEA604 3.1 28.8 1.0
CHB A:HEA604 3.4 26.8 1.0
CHD A:HEA604 3.4 26.3 1.0
CHC A:HEA604 3.5 26.4 1.0
CHA A:HEA604 3.5 26.6 1.0
CG A:HIS61 4.1 23.3 1.0
ND1 A:HIS61 4.1 23.9 1.0
CG A:HIS378 4.2 20.2 1.0
ND1 A:HIS378 4.2 21.1 1.0
C2B A:HEA604 4.2 28.5 1.0
C3D A:HEA604 4.2 26.1 1.0
C3A A:HEA604 4.2 27.6 1.0
C2D A:HEA604 4.2 27.2 1.0
C3B A:HEA604 4.3 29.6 1.0
C3C A:HEA604 4.3 27.5 1.0
C2A A:HEA604 4.3 28.5 1.0
C2C A:HEA604 4.3 27.9 1.0
CE1 A:PHE377 4.8 25.1 1.0

Iron binding site 2 out of 6 in 5iy5

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Iron binding site 2 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe605

b:28.5
occ:1.00
FE A:HEA605 0.0 28.5 1.0
NC A:HEA605 2.0 25.1 1.0
NE2 A:HIS376 2.0 26.2 1.0
O1 A:PER606 2.1 40.3 1.0
ND A:HEA605 2.1 29.1 1.0
NB A:HEA605 2.1 28.8 1.0
NA A:HEA605 2.1 24.3 1.0
O2 A:PER606 3.0 54.0 1.0
C4C A:HEA605 3.0 26.2 1.0
CE1 A:HIS376 3.0 27.1 1.0
C1C A:HEA605 3.1 23.4 1.0
C4A A:HEA605 3.1 23.6 1.0
C4D A:HEA605 3.1 26.2 1.0
C1A A:HEA605 3.1 26.1 1.0
CD2 A:HIS376 3.1 25.7 1.0
C4B A:HEA605 3.1 28.0 1.0
C1B A:HEA605 3.1 29.0 1.0
C1D A:HEA605 3.1 27.6 1.0
CHA A:HEA605 3.4 25.9 1.0
CHB A:HEA605 3.4 25.6 1.0
CHD A:HEA605 3.4 23.9 1.0
CHC A:HEA605 3.5 24.8 1.0
ND1 A:HIS376 4.2 26.8 1.0
CG A:HIS376 4.2 26.4 1.0
C3C A:HEA605 4.3 24.1 1.0
C2C A:HEA605 4.3 24.0 1.0
C3A A:HEA605 4.3 23.9 1.0
C2A A:HEA605 4.3 25.8 1.0
C3D A:HEA605 4.3 24.9 1.0
C3B A:HEA605 4.3 27.8 1.0
C2B A:HEA605 4.3 28.8 1.0
C2D A:HEA605 4.4 24.2 1.0
CU A:CU601 4.9 29.8 1.0
CG2 A:VAL243 4.9 23.2 1.0

Iron binding site 3 out of 6 in 5iy5

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Iron binding site 3 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe605

b:36.5
occ:1.00
FE N:HEA605 0.0 36.5 1.0
NE2 N:HIS61 1.9 33.6 1.0
NE2 N:HIS378 1.9 31.8 1.0
ND N:HEA605 2.0 34.3 1.0
NB N:HEA605 2.1 37.6 1.0
NC N:HEA605 2.1 34.9 1.0
NA N:HEA605 2.1 34.3 1.0
CD2 N:HIS61 2.9 35.5 1.0
CD2 N:HIS378 2.9 31.5 1.0
CE1 N:HIS61 2.9 33.2 1.0
CE1 N:HIS378 3.0 32.9 1.0
C1D N:HEA605 3.0 36.3 1.0
C1B N:HEA605 3.1 39.7 1.0
C4D N:HEA605 3.1 36.1 1.0
C1C N:HEA605 3.1 35.7 1.0
C4C N:HEA605 3.1 36.4 1.0
C1A N:HEA605 3.1 38.8 1.0
C4A N:HEA605 3.1 38.9 1.0
C4B N:HEA605 3.1 36.6 1.0
CHD N:HEA605 3.4 32.2 1.0
CHB N:HEA605 3.5 35.4 1.0
CHC N:HEA605 3.5 32.1 1.0
CHA N:HEA605 3.5 35.5 1.0
ND1 N:HIS61 4.1 35.8 1.0
CG N:HIS61 4.1 35.5 1.0
ND1 N:HIS378 4.1 34.6 1.0
CG N:HIS378 4.1 34.7 1.0
C2B N:HEA605 4.3 44.0 1.0
C3B N:HEA605 4.3 38.3 1.0
C2D N:HEA605 4.3 36.8 1.0
C3A N:HEA605 4.3 35.8 1.0
C3D N:HEA605 4.3 35.3 1.0
C2C N:HEA605 4.3 36.0 1.0
C2A N:HEA605 4.3 39.3 1.0
C3C N:HEA605 4.3 34.8 1.0
CE1 N:PHE377 4.9 37.8 1.0

Iron binding site 4 out of 6 in 5iy5

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Iron binding site 4 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe606

b:35.0
occ:1.00
FE N:HEA606 0.0 35.0 1.0
NB N:HEA606 2.0 30.7 1.0
NE2 N:HIS376 2.0 38.7 1.0
NA N:HEA606 2.1 34.8 1.0
O1 N:PER607 2.1 36.8 1.0
ND N:HEA606 2.1 34.9 1.0
NC N:HEA606 2.1 33.3 1.0
C4B N:HEA606 3.0 30.6 1.0
CD2 N:HIS376 3.0 38.4 1.0
C1B N:HEA606 3.1 33.7 1.0
C1A N:HEA606 3.1 32.1 1.0
C4A N:HEA606 3.1 33.4 1.0
CE1 N:HIS376 3.1 34.9 1.0
C4D N:HEA606 3.1 33.4 1.0
C1D N:HEA606 3.1 35.4 1.0
C1C N:HEA606 3.1 32.6 1.0
C4C N:HEA606 3.1 36.6 1.0
O2 N:PER607 3.2 48.7 1.0
CHB N:HEA606 3.4 31.3 1.0
CHC N:HEA606 3.5 30.1 1.0
CHA N:HEA606 3.5 31.3 1.0
CHD N:HEA606 3.5 35.2 1.0
ND1 N:HIS376 4.2 37.0 1.0
CG N:HIS376 4.2 33.9 1.0
C3B N:HEA606 4.3 31.9 1.0
C3A N:HEA606 4.3 33.6 1.0
C2A N:HEA606 4.3 35.2 1.0
C2B N:HEA606 4.3 33.2 1.0
C3D N:HEA606 4.3 33.6 1.0
C2D N:HEA606 4.3 33.0 1.0
C2C N:HEA606 4.3 29.8 1.0
C3C N:HEA606 4.4 31.2 1.0
CU N:CU602 4.8 35.9 1.0
CG2 N:VAL243 4.9 27.9 1.0

Iron binding site 5 out of 6 in 5iy5

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Iron binding site 5 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe201

b:75.0
occ:1.00
FE 1:HEC201 0.0 75.0 1.0
ND 1:HEC201 1.9 83.2 1.0
NA 1:HEC201 2.0 89.9 1.0
NE2 1:HIS18 2.1 76.5 1.0
NB 1:HEC201 2.1 78.1 1.0
NC 1:HEC201 2.1 74.5 1.0
SD 1:MET80 2.6 81.3 1.0
C4D 1:HEC201 2.9 82.8 1.0
C1D 1:HEC201 3.0 82.5 1.0
CE1 1:HIS18 3.0 80.9 1.0
C1A 1:HEC201 3.0 87.1 1.0
C4B 1:HEC201 3.0 73.0 1.0
C1B 1:HEC201 3.1 79.0 1.0
C4A 1:HEC201 3.1 87.6 1.0
C4C 1:HEC201 3.1 77.0 1.0
C1C 1:HEC201 3.1 70.5 1.0
CD2 1:HIS18 3.1 79.5 1.0
CHA 1:HEC201 3.4 87.1 1.0
CHC 1:HEC201 3.4 74.1 1.0
CHD 1:HEC201 3.5 80.0 1.0
CHB 1:HEC201 3.5 80.3 1.0
CE 1:MET80 3.6 79.2 1.0
CG 1:MET80 3.7 85.3 1.0
ND1 1:HIS18 4.2 80.2 1.0
C3D 1:HEC201 4.2 89.2 1.0
CB 1:MET80 4.2 85.3 1.0
C2A 1:HEC201 4.2 90.5 1.0
C2D 1:HEC201 4.2 87.5 1.0
C3A 1:HEC201 4.3 86.1 1.0
CG 1:HIS18 4.3 76.5 1.0
C3B 1:HEC201 4.3 72.8 1.0
C2B 1:HEC201 4.3 75.7 1.0
C2C 1:HEC201 4.3 66.5 1.0
C3C 1:HEC201 4.3 70.2 1.0
OH 1:TYR67 4.7 73.2 1.0

Iron binding site 6 out of 6 in 5iy5

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Iron binding site 6 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe201

b:0.8
occ:1.00
FE 2:HEC201 0.0 0.8 1.0
ND 2:HEC201 1.9 0.3 1.0
NA 2:HEC201 2.0 0.8 1.0
NB 2:HEC201 2.1 97.1 1.0
NC 2:HEC201 2.1 93.7 1.0
SD 2:MET80 2.6 93.5 1.0
NE2 2:HIS18 2.6 0.4 1.0
C4D 2:HEC201 2.9 0.7 1.0
C1D 2:HEC201 2.9 0.8 1.0
C1A 2:HEC201 3.0 0.1 1.0
C4A 2:HEC201 3.0 0.1 1.0
C4C 2:HEC201 3.1 95.5 1.0
C1B 2:HEC201 3.1 98.4 1.0
CD2 2:HIS18 3.1 0.9 1.0
C4B 2:HEC201 3.1 90.0 1.0
C1C 2:HEC201 3.2 87.8 1.0
CHA 2:HEC201 3.4 0.0 1.0
CHD 2:HEC201 3.4 0.3 1.0
CHB 2:HEC201 3.4 0.9 1.0
CHC 2:HEC201 3.6 84.3 1.0
CE 2:MET80 3.7 93.1 1.0
CE1 2:HIS18 3.8 0.1 1.0
CG 2:MET80 3.8 1.0 1.0
C2A 2:HEC201 4.2 0.3 1.0
C2D 2:HEC201 4.2 0.8 1.0
C3D 2:HEC201 4.2 0.8 1.0
C3A 2:HEC201 4.2 0.7 1.0
CB 2:MET80 4.3 97.7 1.0
C3C 2:HEC201 4.3 89.9 1.0
C2B 2:HEC201 4.3 91.9 1.0
CG 2:HIS18 4.3 0.5 1.0
C2C 2:HEC201 4.4 88.8 1.0
C3B 2:HEC201 4.4 88.9 1.0
ND1 2:HIS18 4.6 0.7 1.0

Reference:

S.Shimada, K.Shinzawa-Itoh, J.Baba, S.Aoe, A.Shimada, E.Yamashita, J.Kang, M.Tateno, S.Yoshikawa, T.Tsukihara. Complex Structure of Cytochrome C-Cytochrome C Oxidase Reveals A Novel Protein-Protein Interaction Mode Embo J. V. 36 291 2017.
ISSN: ESSN 1460-2075
PubMed: 27979921
DOI: 10.15252/EMBJ.201695021
Page generated: Sun Dec 13 16:03:59 2020

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