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Copper 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
Iron (Fe) 2 atoms
Calcium (Ca) 1 atom

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 3 binding sites of Copper 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 Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 1qle

Go back to Copper Binding Sites List in 1qle
Copper binding site 1 out of 3 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 Copper with other atoms in the Cu 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:Cu603

b:11.8
occ:1.00
NE2 A:HIS326 2.1 20.7 1.0
ND1 A:HIS276 2.1 12.1 1.0
NE2 A:HIS325 2.2 27.5 1.0
CE1 A:HIS326 2.9 26.3 1.0
CE1 A:HIS325 3.1 31.3 1.0
CG A:HIS276 3.1 10.6 1.0
CE1 A:HIS276 3.2 12.0 1.0
CD2 A:HIS326 3.2 20.3 1.0
CD2 A:HIS325 3.3 30.7 1.0
CB A:HIS276 3.4 9.6 1.0
CA A:HIS276 3.9 17.5 1.0
ND1 A:HIS326 4.1 27.5 1.0
CG A:HIS326 4.2 24.0 1.0
CD2 A:HIS276 4.3 14.4 1.0
ND1 A:HIS325 4.3 32.7 1.0
NE2 A:HIS276 4.3 12.3 1.0
CG A:HIS325 4.4 29.9 1.0
NA A:HEA602 4.5 19.1 1.0
C1A A:HEA602 4.5 23.1 1.0
N A:HIS276 4.7 16.1 1.0
C4A A:HEA602 4.7 15.6 1.0
CHA A:HEA602 4.8 25.3 1.0
ND A:HEA602 4.9 20.6 1.0
C2A A:HEA602 4.9 19.3 1.0
C A:HIS276 5.0 22.9 1.0
CG1 A:VAL279 5.0 8.3 1.0

Copper binding site 2 out of 3 in 1qle

Go back to Copper Binding Sites List in 1qle
Copper binding site 2 out of 3 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 Copper with other atoms in the Cu 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
B:Cu301

b:32.5
occ:1.00
CU1 B:CUA301 0.0 32.5 1.0
ND1 B:HIS224 2.0 18.5 1.0
SG B:CYS220 2.1 35.3 1.0
SG B:CYS216 2.1 25.7 1.0
CU2 B:CUA301 2.5 26.7 1.0
CE1 B:HIS224 3.0 18.5 1.0
CG B:HIS224 3.1 25.5 1.0
O B:GLU218 3.1 36.8 1.0
CB B:CYS220 3.3 39.0 1.0
CB B:CYS216 3.3 19.3 1.0
CB B:HIS224 3.5 35.7 1.0
CA B:HIS224 3.6 40.0 1.0
N B:CYS220 3.6 35.4 1.0
O B:HIS224 3.9 39.9 1.0
CA B:CYS220 4.1 34.2 1.0
C B:GLU218 4.1 34.8 1.0
NE2 B:HIS224 4.2 22.3 1.0
C B:HIS224 4.2 40.0 1.0
CD2 B:HIS224 4.2 21.3 1.0
SD B:MET227 4.3 44.6 1.0
C B:LEU219 4.4 35.5 1.0
ND1 B:HIS181 4.4 30.8 1.0
CA B:CYS216 4.6 21.9 1.0
CA B:LEU219 4.6 33.1 1.0
CG B:MET227 4.6 41.3 1.0
C B:CYS216 4.7 21.4 1.0
N B:LEU219 4.7 31.7 1.0
N B:GLU218 4.7 29.9 1.0
O B:CYS216 4.8 28.6 1.0
N B:HIS224 4.8 43.2 1.0
C B:CYS220 4.9 36.0 1.0

Copper binding site 3 out of 3 in 1qle

Go back to Copper Binding Sites List in 1qle
Copper binding site 3 out of 3 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 Copper with other atoms in the Cu binding site number 3 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
B:Cu301

b:26.7
occ:1.00
CU2 B:CUA301 0.0 26.7 1.0
ND1 B:HIS181 2.1 30.8 1.0
SG B:CYS220 2.1 35.3 1.0
SG B:CYS216 2.2 25.7 1.0
CU1 B:CUA301 2.5 32.5 1.0
SD B:MET227 2.6 44.6 1.0
CE1 B:HIS181 3.0 32.7 1.0
CG B:HIS181 3.2 32.7 1.0
CB B:CYS220 3.3 39.0 1.0
CE B:MET227 3.5 46.6 1.0
CB B:HIS181 3.6 26.9 1.0
CG B:MET227 3.8 41.3 1.0
CB B:CYS216 3.8 19.3 1.0
CA B:HIS181 4.2 29.9 1.0
NE2 B:HIS181 4.2 29.0 1.0
CD2 B:HIS181 4.3 31.4 1.0
ND1 B:HIS224 4.5 18.5 1.0
O B:GLU218 4.5 36.8 1.0
CA B:CYS220 4.7 34.2 1.0
O B:HIS119 4.7 46.7 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: Sun Dec 13 11:01:35 2020

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