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Iron in PDB 8dh6: Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs

Enzymatic activity of Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs

All present enzymatic activity of Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs:
7.1.1.9;

Other elements in 8dh6:

The structure of Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Copper (Cu) 2 atoms
Calcium (Ca) 1 atom
Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs (pdb code 8dh6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs, PDB code: 8dh6:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 8dh6

Go back to Iron Binding Sites List in 8dh6
Iron binding site 1 out of 2 in the Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe604

b:54.3
occ:1.00
FE a:HEA604 0.0 54.3 1.0
NE2 a:HIS62 1.8 50.1 1.0
NA a:HEA604 2.0 54.3 1.0
NC a:HEA604 2.1 54.3 1.0
NB a:HEA604 2.1 54.3 1.0
ND a:HEA604 2.1 54.3 1.0
NE2 a:HIS378 2.2 51.2 1.0
CD2 a:HIS62 2.8 50.1 1.0
CE1 a:HIS62 2.8 50.1 1.0
C4A a:HEA604 3.0 54.3 1.0
C1A a:HEA604 3.0 54.3 1.0
C4C a:HEA604 3.1 54.3 1.0
C1B a:HEA604 3.1 54.3 1.0
C1C a:HEA604 3.1 54.3 1.0
C1D a:HEA604 3.1 54.3 1.0
C4B a:HEA604 3.1 54.3 1.0
C4D a:HEA604 3.1 54.3 1.0
CE1 a:HIS378 3.2 51.2 1.0
CD2 a:HIS378 3.2 51.2 1.0
CHB a:HEA604 3.4 54.3 1.0
CHD a:HEA604 3.4 54.3 1.0
CHA a:HEA604 3.5 54.3 1.0
CHC a:HEA604 3.5 54.3 1.0
ND1 a:HIS62 3.9 50.1 1.0
CG a:HIS62 3.9 50.1 1.0
C3A a:HEA604 4.1 54.3 1.0
C2A a:HEA604 4.1 54.3 1.0
ND1 a:HIS378 4.3 51.2 1.0
CG a:HIS378 4.3 51.2 1.0
C3C a:HEA604 4.4 54.3 1.0
C2B a:HEA604 4.4 54.3 1.0
C2C a:HEA604 4.4 54.3 1.0
C2D a:HEA604 4.4 54.3 1.0
C3B a:HEA604 4.4 54.3 1.0
C3D a:HEA604 4.5 54.3 1.0

Iron binding site 2 out of 2 in 8dh6

Go back to Iron Binding Sites List in 8dh6
Iron binding site 2 out of 2 in the Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe605

b:54.3
occ:1.00
FE a:HEA605 0.0 54.3 1.0
NA a:HEA605 2.0 54.3 1.0
NC a:HEA605 2.1 54.3 1.0
ND a:HEA605 2.1 54.3 1.0
NB a:HEA605 2.1 54.3 1.0
NE2 a:HIS376 2.5 50.5 1.0
C1A a:HEA605 3.0 54.3 1.0
C4A a:HEA605 3.0 54.3 1.0
C1C a:HEA605 3.1 54.3 1.0
C4B a:HEA605 3.1 54.3 1.0
C4D a:HEA605 3.1 54.3 1.0
C1D a:HEA605 3.1 54.3 1.0
C4C a:HEA605 3.1 54.3 1.0
C1B a:HEA605 3.1 54.3 1.0
CD2 a:HIS376 3.3 50.5 1.0
CHA a:HEA605 3.4 54.3 1.0
CHC a:HEA605 3.5 54.3 1.0
CHB a:HEA605 3.5 54.3 1.0
CHD a:HEA605 3.5 54.3 1.0
CE1 a:HIS376 3.5 50.5 1.0
C3A a:HEA605 4.2 54.3 1.0
C2A a:HEA605 4.2 54.3 1.0
C3C a:HEA605 4.4 54.3 1.0
C2C a:HEA605 4.4 54.3 1.0
C2B a:HEA605 4.4 54.3 1.0
C2D a:HEA605 4.4 54.3 1.0
C3B a:HEA605 4.4 54.3 1.0
C3D a:HEA605 4.4 54.3 1.0
CU a:CU603 4.5 66.3 1.0
CG a:HIS376 4.5 50.5 1.0
CE1 a:HIS241 4.6 56.8 1.0
ND1 a:HIS376 4.6 50.5 1.0
CG2 a:VAL380 4.9 52.1 1.0

Reference:

A.S.Godoy, Y.Song, H.Cheruvara, A.Quigley, G.Oliva. Cryo-Em Structure of Saccharomyces Cerevisiae Cytochrome C Oxidase (Complex IV) Extracted in Lipid Nanodiscs To Be Published.
Page generated: Fri Aug 9 23:30:03 2024

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