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Iron in PDB 5b1a: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 5b1a was solved by N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.938, 204.400, 177.896, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.2

Other elements in 5b1a:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution 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 in the Fully Oxidized State at 1.5 Angstrom Resolution (pdb code 5b1a). 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 in the Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 5b1a:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5b1a

Go back to Iron Binding Sites List in 5b1a
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution


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 in the Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:18.9
occ:1.00
 FE A:HEA601 0.0 18.9 1.0
NE2 A:HIS378 2.0 17.4 1.0
NB A:HEA601 2.0 19.0 1.0
NE2 A:HIS61 2.0 17.4 1.0
NC A:HEA601 2.0 17.7 1.0
ND A:HEA601 2.0 17.6 1.0
NA A:HEA601 2.0 17.8 1.0
CE1 A:HIS61 2.9 18.8 1.0
CE1 A:HIS378 3.0 18.7 1.0
C4A A:HEA601 3.0 18.3 1.0
C4C A:HEA601 3.0 17.4 1.0
C1B A:HEA601 3.0 18.0 1.0
C1D A:HEA601 3.0 17.1 1.0
C4D A:HEA601 3.0 17.9 1.0
C1C A:HEA601 3.0 18.1 1.0
C4B A:HEA601 3.0 18.6 1.0
C1A A:HEA601 3.1 18.9 1.0
CD2 A:HIS378 3.1 19.5 1.0
CD2 A:HIS61 3.1 18.6 1.0
CHC A:HEA601 3.4 18.4 1.0
CHD A:HEA601 3.4 18.1 1.0
CHB A:HEA601 3.5 19.7 1.0
CHA A:HEA601 3.5 18.7 1.0
CG A:HIS61 4.2 19.6 1.0
ND1 A:HIS61 4.2 19.1 1.0
ND1 A:HIS378 4.2 18.2 1.0
CG A:HIS378 4.2 17.6 1.0
C3A A:HEA601 4.2 18.3 1.0
C2C A:HEA601 4.2 18.2 1.0
C2A A:HEA601 4.2 19.5 1.0
C3C A:HEA601 4.2 17.6 1.0
C3D A:HEA601 4.3 17.7 1.0
C3B A:HEA601 4.3 17.6 1.0
C2B A:HEA601 4.3 17.9 1.0
C2D A:HEA601 4.3 18.2 1.0
CE2 A:PHE377 4.8 19.0 1.0

Iron binding site 2 out of 4 in 5b1a

Go back to Iron Binding Sites List in 5b1a
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution


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 in the Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:18.4
occ:1.00
 FE A:HEA602 0.0 18.4 1.0
NC A:HEA602 2.0 18.1 1.0
NA A:HEA602 2.0 17.7 1.0
ND A:HEA602 2.0 18.1 1.0
NB A:HEA602 2.1 17.7 1.0
NE2 A:HIS376 2.1 18.2 1.0
O1 A:PER606 2.3 17.6 1.0
C4A A:HEA602 3.0 18.6 1.0
C4B A:HEA602 3.1 18.1 1.0
C1D A:HEA602 3.1 18.4 1.0
C1B A:HEA602 3.1 19.1 1.0
C1C A:HEA602 3.1 18.2 1.0
C4D A:HEA602 3.1 17.8 1.0
C4C A:HEA602 3.1 18.0 1.0
C1A A:HEA602 3.1 17.9 1.0
CE1 A:HIS376 3.1 18.3 1.0
CD2 A:HIS376 3.2 17.7 1.0
CHD A:HEA602 3.4 17.9 1.0
CHA A:HEA602 3.5 18.7 1.0
CHB A:HEA602 3.5 19.6 1.0
CHC A:HEA602 3.5 17.5 1.0
O2 A:PER606 3.7 22.5 1.0
ND1 A:HIS376 4.2 18.7 1.0
C3B A:HEA602 4.3 17.7 1.0
C3A A:HEA602 4.3 17.5 1.0
C2D A:HEA602 4.3 18.6 1.0
C3C A:HEA602 4.3 17.9 1.0
C2A A:HEA602 4.3 18.0 1.0
C2C A:HEA602 4.3 18.4 1.0
C2B A:HEA602 4.3 18.4 1.0
CG A:HIS376 4.3 18.2 1.0
C3D A:HEA602 4.3 18.1 1.0
CU A:CU603 4.8 19.0 1.0
CG2 A:VAL243 5.0 18.4 1.0

Iron binding site 3 out of 4 in 5b1a

Go back to Iron Binding Sites List in 5b1a
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution


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 in the Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:23.3
occ:1.00
 FE N:HEA601 0.0 23.3 1.0
NC N:HEA601 2.0 22.2 1.0
ND N:HEA601 2.0 22.1 1.0
NB N:HEA601 2.0 23.0 1.0
NE2 N:HIS61 2.0 22.5 1.0
NA N:HEA601 2.0 23.1 1.0
NE2 N:HIS378 2.0 22.5 1.0
CE1 N:HIS61 3.0 23.8 1.0
CE1 N:HIS378 3.0 23.5 1.0
C4A N:HEA601 3.0 23.9 1.0
C1D N:HEA601 3.0 22.9 1.0
C4B N:HEA601 3.0 23.8 1.0
C1C N:HEA601 3.0 23.8 1.0
C4C N:HEA601 3.0 21.8 1.0
CD2 N:HIS61 3.1 23.7 1.0
CD2 N:HIS378 3.1 22.4 1.0
C1A N:HEA601 3.1 22.5 1.0
C1B N:HEA601 3.1 23.3 1.0
C4D N:HEA601 3.1 23.8 1.0
CHD N:HEA601 3.4 22.4 1.0
CHC N:HEA601 3.5 22.6 1.0
CHB N:HEA601 3.5 24.5 1.0
CHA N:HEA601 3.5 23.5 1.0
ND1 N:HIS378 4.1 23.5 1.0
ND1 N:HIS61 4.1 23.6 1.0
CG N:HIS61 4.1 23.9 1.0
CG N:HIS378 4.2 22.1 1.0
C3A N:HEA601 4.2 23.8 1.0
C3B N:HEA601 4.2 22.2 1.0
C2D N:HEA601 4.2 21.4 1.0
C2C N:HEA601 4.3 22.2 1.0
C2B N:HEA601 4.3 23.6 1.0
C3D N:HEA601 4.3 21.8 1.0
C2A N:HEA601 4.3 24.0 1.0
C3C N:HEA601 4.3 21.2 1.0
CE2 N:PHE377 4.8 21.3 1.0

Iron binding site 4 out of 4 in 5b1a

Go back to Iron Binding Sites List in 5b1a
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution


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 in the Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:21.2
occ:1.00
 FE N:HEA602 0.0 21.2 1.0
ND N:HEA602 2.0 21.1 1.0
NA N:HEA602 2.0 20.2 1.0
NC N:HEA602 2.0 21.5 1.0
NB N:HEA602 2.1 20.2 1.0
NE2 N:HIS376 2.1 21.4 1.0
O1 N:PER606 2.3 20.7 1.0
C1D N:HEA602 3.0 21.2 1.0
C1C N:HEA602 3.0 20.8 1.0
C4A N:HEA602 3.1 21.1 1.0
C1B N:HEA602 3.1 21.4 1.0
C1A N:HEA602 3.1 22.0 1.0
C4B N:HEA602 3.1 19.1 1.0
CE1 N:HIS376 3.1 22.0 1.0
C4C N:HEA602 3.1 21.4 1.0
C4D N:HEA602 3.1 21.8 1.0
CD2 N:HIS376 3.2 21.8 1.0
CHA N:HEA602 3.4 20.6 1.0
CHD N:HEA602 3.5 21.0 1.0
CHB N:HEA602 3.5 20.0 1.0
CHC N:HEA602 3.5 20.6 1.0
O2 N:PER606 3.7 26.2 1.0
ND1 N:HIS376 4.2 21.9 1.0
C2C N:HEA602 4.2 20.6 1.0
C3A N:HEA602 4.2 21.3 1.0
C2D N:HEA602 4.3 21.2 1.0
C3B N:HEA602 4.3 20.4 1.0
CG N:HIS376 4.3 22.0 1.0
C3C N:HEA602 4.3 20.6 1.0
C2A N:HEA602 4.3 21.0 1.0
C2B N:HEA602 4.3 21.2 1.0
C3D N:HEA602 4.3 21.2 1.0
CU N:CU603 4.8 21.7 1.0
CG2 N:VAL243 5.0 19.9 1.0

Reference:

N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, S.Yoshikawa. The MG2+-Containing Water Cluster of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J.Biol.Chem. V. 291 23882 2016.
ISSN: ESSN 1083-351X
PubMed: 27605664
DOI: 10.1074/JBC.M115.711770
Page generated: Mon Aug 5 19:59:56 2024

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