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Iron in PDB 1qle: Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment

Enzymatic activity of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment

All present enzymatic activity of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment:
1.9.3.1;

Protein crystallography data

The structure of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment, PDB code: 1qle was solved by A.Harrenga, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 3.00
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 205.200, 205.200, 81.100, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 30.9

Other elements in 1qle:

The structure of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Copper (Cu) 3 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment (pdb code 1qle). 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-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment, PDB code: 1qle:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 1qle

Go back to Iron Binding Sites List in 1qle
Iron binding site 1 out of 2 in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:20.5
occ:1.00
FE A:HEA601 0.0 20.5 1.0
NC A:HEA601 2.0 23.2 1.0
NA A:HEA601 2.0 26.4 1.0
ND A:HEA601 2.0 23.5 1.0
NB A:HEA601 2.0 25.1 1.0
NE2 A:HIS413 2.2 14.4 1.0
NE2 A:HIS94 2.2 22.2 1.0
C1A A:HEA601 3.0 24.0 1.0
C1C A:HEA601 3.0 24.7 1.0
C4C A:HEA601 3.0 23.8 1.0
C4A A:HEA601 3.0 27.6 1.0
C1D A:HEA601 3.0 24.9 1.0
C4D A:HEA601 3.0 23.9 1.0
C4B A:HEA601 3.0 26.4 1.0
C1B A:HEA601 3.1 27.2 1.0
CE1 A:HIS413 3.1 14.6 1.0
CD2 A:HIS413 3.2 18.3 1.0
CE1 A:HIS94 3.2 18.3 1.0
CD2 A:HIS94 3.3 19.0 1.0
CHA A:HEA601 3.4 23.8 1.0
CHD A:HEA601 3.4 21.2 1.0
CHC A:HEA601 3.4 21.9 1.0
CHB A:HEA601 3.4 28.1 1.0
C2C A:HEA601 4.2 32.6 1.0
C2A A:HEA601 4.2 22.2 1.0
C3A A:HEA601 4.2 25.5 1.0
C3C A:HEA601 4.3 31.1 1.0
C2D A:HEA601 4.3 16.4 1.0
C3D A:HEA601 4.3 17.7 1.0
C3B A:HEA601 4.3 26.7 1.0
ND1 A:HIS413 4.3 21.7 1.0
C2B A:HEA601 4.3 24.8 1.0
CG A:HIS413 4.3 15.0 1.0
ND1 A:HIS94 4.4 17.5 1.0
CG A:HIS94 4.4 18.6 1.0
CG2 A:THR50 4.7 17.6 1.0
CE1 A:PHE412 4.7 10.3 1.0

Iron binding site 2 out of 2 in 1qle

Go back to Iron Binding Sites List in 1qle
Iron binding site 2 out of 2 in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:23.0
occ:1.00
FE A:HEA602 0.0 23.0 1.0
ND A:HEA602 2.0 20.6 1.0
NC A:HEA602 2.0 20.7 1.0
NA A:HEA602 2.0 19.1 1.0
NB A:HEA602 2.0 21.8 1.0
NE2 A:HIS411 2.2 17.3 1.0
C4D A:HEA602 3.0 21.2 1.0
C1A A:HEA602 3.0 23.1 1.0
C1D A:HEA602 3.0 18.5 1.0
C1C A:HEA602 3.0 21.4 1.0
C4B A:HEA602 3.1 17.5 1.0
C4C A:HEA602 3.1 21.5 1.0
C4A A:HEA602 3.1 15.6 1.0
C1B A:HEA602 3.1 20.6 1.0
CE1 A:HIS411 3.2 9.8 1.0
CD2 A:HIS411 3.2 15.6 1.0
CHA A:HEA602 3.4 25.3 1.0
CHC A:HEA602 3.4 17.9 1.0
CHD A:HEA602 3.4 15.8 1.0
CHB A:HEA602 3.5 17.3 1.0
C3D A:HEA602 4.3 16.2 1.0
C2A A:HEA602 4.3 19.3 1.0
C2D A:HEA602 4.3 12.5 1.0
C3B A:HEA602 4.3 15.9 1.0
C2C A:HEA602 4.3 19.6 1.0
C3C A:HEA602 4.3 22.4 1.0
C2B A:HEA602 4.3 16.5 1.0
C3A A:HEA602 4.3 12.1 1.0
ND1 A:HIS411 4.3 10.5 1.0
CG A:HIS411 4.4 16.3 1.0

Reference:

A.Harrenga, H.Michel. The Cytochrome C Oxidase From Paracoccus Denitrificans Does Not Change the Metal Center Ligation Upon Reduction J.Biol.Chem. V. 274 33296 1999.
ISSN: ISSN 0021-9258
PubMed: 10559205
DOI: 10.1074/JBC.274.47.33296
Page generated: Sat Aug 3 13:33:32 2024

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