Atomistry » Copper » PDB 1oe2-1rjp » 1qle
Atomistry »
  Copper »
    PDB 1oe2-1rjp »
      1qle »

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: Tue Jul 30 22:37:16 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy