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Iron in PDB 1v55: Bovine Heart Cytochrome C Oxidase at the Fully Reduced State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State, PDB code: 1v55 was solved by T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.060, 206.584, 178.298, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 23

Other elements in 1v55:

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State 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 Bovine Heart Cytochrome C Oxidase at the Fully Reduced State (pdb code 1v55). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced State, PDB code: 1v55:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1v55

Go back to Iron Binding Sites List in 1v55
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:15.8
occ:1.00
FE A:HEA515 0.0 15.8 1.0
NB A:HEA515 1.9 19.1 1.0
NE2 A:HIS378 2.0 11.6 1.0
ND A:HEA515 2.0 19.0 1.0
NC A:HEA515 2.0 20.9 1.0
NE2 A:HIS61 2.0 12.9 1.0
NA A:HEA515 2.0 19.7 1.0
CE1 A:HIS378 2.8 13.5 1.0
CE1 A:HIS61 3.0 14.4 1.0
C4B A:HEA515 3.0 21.2 1.0
C1B A:HEA515 3.0 18.2 1.0
C4C A:HEA515 3.1 20.7 1.0
C4A A:HEA515 3.1 19.6 1.0
C1D A:HEA515 3.1 18.9 1.0
C1C A:HEA515 3.1 18.2 1.0
C4D A:HEA515 3.1 20.2 1.0
C1A A:HEA515 3.1 20.3 1.0
CD2 A:HIS61 3.1 16.1 1.0
CD2 A:HIS378 3.1 11.4 1.0
CHC A:HEA515 3.4 17.7 1.0
CHB A:HEA515 3.4 18.6 1.0
CHD A:HEA515 3.5 17.5 1.0
CHA A:HEA515 3.5 19.5 1.0
ND1 A:HIS378 4.0 13.4 1.0
ND1 A:HIS61 4.2 12.6 1.0
CG A:HIS378 4.2 11.2 1.0
C3B A:HEA515 4.2 21.1 1.0
CG A:HIS61 4.2 14.4 1.0
C2B A:HEA515 4.2 18.6 1.0
C2A A:HEA515 4.3 20.8 1.0
C3D A:HEA515 4.3 19.0 1.0
C2D A:HEA515 4.3 17.9 1.0
C3A A:HEA515 4.3 18.6 1.0
C3C A:HEA515 4.3 17.1 1.0
C2C A:HEA515 4.3 17.5 1.0
OG A:SER382 4.6 41.2 1.0
CE2 A:PHE377 4.9 16.6 1.0

Iron binding site 2 out of 4 in 1v55

Go back to Iron Binding Sites List in 1v55
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:17.6
occ:1.00
FE A:HEA516 0.0 17.6 1.0
NB A:HEA516 1.9 16.7 1.0
ND A:HEA516 1.9 15.5 1.0
NA A:HEA516 2.1 16.2 1.0
NC A:HEA516 2.1 17.3 1.0
NE2 A:HIS376 2.2 18.6 1.0
C4B A:HEA516 3.0 21.4 1.0
C4D A:HEA516 3.0 19.9 1.0
C1B A:HEA516 3.0 19.1 1.0
CE1 A:HIS376 3.0 19.4 1.0
C1D A:HEA516 3.1 18.2 1.0
C1A A:HEA516 3.1 14.7 1.0
C4A A:HEA516 3.1 16.9 1.0
C1C A:HEA516 3.1 16.8 1.0
C4C A:HEA516 3.2 15.6 1.0
CD2 A:HIS376 3.3 16.6 1.0
CHC A:HEA516 3.4 18.0 1.0
CHA A:HEA516 3.4 14.9 1.0
CHB A:HEA516 3.4 19.2 1.0
CHD A:HEA516 3.5 12.9 1.0
C3D A:HEA516 4.2 16.4 1.0
ND1 A:HIS376 4.2 18.5 1.0
C2B A:HEA516 4.2 17.5 1.0
C3B A:HEA516 4.3 19.3 1.0
C2D A:HEA516 4.3 17.1 1.0
C2A A:HEA516 4.3 16.1 1.0
CG A:HIS376 4.3 16.6 1.0
C3A A:HEA516 4.3 17.0 1.0
C2C A:HEA516 4.4 17.3 1.0
C3C A:HEA516 4.4 16.7 1.0
CG2 A:VAL380 4.8 21.2 1.0

Iron binding site 3 out of 4 in 1v55

Go back to Iron Binding Sites List in 1v55
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:19.8
occ:1.00
FE N:HEA515 0.0 19.8 1.0
NB N:HEA515 1.9 26.1 1.0
ND N:HEA515 2.0 23.7 1.0
NA N:HEA515 2.0 22.6 1.0
NC N:HEA515 2.0 23.6 1.0
NE2 N:HIS61 2.0 17.6 1.0
NE2 N:HIS378 2.0 15.6 1.0
CE1 N:HIS378 2.9 16.5 1.0
CE1 N:HIS61 3.0 20.3 1.0
C4B N:HEA515 3.0 25.7 1.0
C4D N:HEA515 3.0 23.4 1.0
C1B N:HEA515 3.0 23.6 1.0
C4A N:HEA515 3.0 23.4 1.0
C1A N:HEA515 3.0 22.4 1.0
C1D N:HEA515 3.0 23.0 1.0
CD2 N:HIS61 3.1 21.5 1.0
C4C N:HEA515 3.1 26.3 1.0
C1C N:HEA515 3.1 25.7 1.0
CD2 N:HIS378 3.2 14.2 1.0
CHB N:HEA515 3.4 23.5 1.0
CHA N:HEA515 3.4 22.9 1.0
CHC N:HEA515 3.4 24.2 1.0
CHD N:HEA515 3.5 21.7 1.0
ND1 N:HIS378 4.1 14.6 1.0
ND1 N:HIS61 4.2 17.4 1.0
CG N:HIS61 4.2 18.9 1.0
C3B N:HEA515 4.2 26.3 1.0
C2A N:HEA515 4.3 21.4 1.0
C2B N:HEA515 4.3 25.9 1.0
C3A N:HEA515 4.3 23.8 1.0
CG N:HIS378 4.3 14.7 1.0
C3D N:HEA515 4.3 22.2 1.0
C2D N:HEA515 4.3 23.6 1.0
C3C N:HEA515 4.4 23.2 1.0
C2C N:HEA515 4.4 23.9 1.0
OG N:SER382 4.6 42.8 1.0
CE2 N:PHE377 5.0 18.1 1.0

Iron binding site 4 out of 4 in 1v55

Go back to Iron Binding Sites List in 1v55
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:19.1
occ:1.00
FE N:HEA516 0.0 19.1 1.0
ND N:HEA516 1.9 17.1 1.0
NB N:HEA516 2.0 19.0 1.0
NA N:HEA516 2.1 19.1 1.0
NC N:HEA516 2.1 19.6 1.0
NE2 N:HIS376 2.2 20.4 1.0
C4D N:HEA516 3.0 18.8 1.0
C1D N:HEA516 3.0 19.6 1.0
C4B N:HEA516 3.0 20.2 1.0
C1B N:HEA516 3.1 19.3 1.0
C1A N:HEA516 3.1 19.3 1.0
C1C N:HEA516 3.1 19.4 1.0
CE1 N:HIS376 3.1 22.9 1.0
C4A N:HEA516 3.1 18.9 1.0
C4C N:HEA516 3.1 21.6 1.0
CD2 N:HIS376 3.3 21.5 1.0
CHA N:HEA516 3.4 18.2 1.0
CHC N:HEA516 3.4 20.2 1.0
CHB N:HEA516 3.5 18.0 1.0
CHD N:HEA516 3.5 19.6 1.0
C3D N:HEA516 4.2 17.0 1.0
C2D N:HEA516 4.2 17.7 1.0
C3B N:HEA516 4.3 19.6 1.0
C2B N:HEA516 4.3 18.6 1.0
ND1 N:HIS376 4.3 23.0 1.0
C2A N:HEA516 4.3 18.8 1.0
C3A N:HEA516 4.4 17.9 1.0
C2C N:HEA516 4.4 20.0 1.0
CG N:HIS376 4.4 22.9 1.0
C3C N:HEA516 4.4 20.0 1.0
CG2 N:VAL380 4.7 23.4 1.0

Reference:

T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa. The Low-Spin Heme of Cytochrome C Oxidase As the Driving Element of the Proton-Pumping Process. Proc.Natl.Acad.Sci.Usa V. 100 15304 2003.
ISSN: ISSN 0027-8424
PubMed: 14673090
DOI: 10.1073/PNAS.2635097100
Page generated: Sun Dec 13 14:34:06 2020

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