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Copper in PDB 9gdf: Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction

Enzymatic activity of Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction

All present enzymatic activity of Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction:
1.9.3.1; 7.1.1.9;

Protein crystallography data

The structure of Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction, PDB code: 9gdf was solved by A.Kabbinale, J.Johannesson, D.Finke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.54 / 2.28
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.688, 98.34, 94.085, 90, 127.58, 90
R / Rfree (%) 15.3 / 19.7

Other elements in 9gdf:

The structure of Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction (pdb code 9gdf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction, PDB code: 9gdf:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 9gdf

Go back to Copper Binding Sites List in 9gdf
Copper binding site 1 out of 3 in the Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:39.0
occ:1.00
 ND1 A:HIS233 2.0 34.2 1.0
NE2 A:HIS282 2.1 40.6 1.0
NE2 A:HIS283 2.1 35.7 1.0
CL A:CL617 2.2 47.0 1.0
CE1 A:HIS282 2.9 43.5 1.0
CE1 A:HIS283 3.0 42.2 1.0
CG A:HIS233 3.0 33.3 1.0
CE1 A:HIS233 3.0 39.1 1.0
CD2 A:HIS283 3.1 37.9 1.0
CD2 A:HIS282 3.2 41.0 1.0
CB A:HIS233 3.4 34.5 1.0
CA A:HIS233 3.6 34.1 1.0
ND1 A:HIS283 4.1 35.8 1.0
ND1 A:HIS282 4.1 35.6 1.0
NE2 A:HIS233 4.1 37.6 1.0
CD2 A:HIS233 4.2 33.0 1.0
CG A:HIS283 4.2 34.5 1.0
C1D A:HAS603 4.2 36.0 1.0
ND A:HAS603 4.2 33.8 1.0
CG A:HIS282 4.2 34.9 1.0
C4D A:HAS603 4.4 34.9 1.0
C2D A:HAS603 4.5 38.5 1.0
N A:HIS233 4.5 32.2 1.0
C A:HIS233 4.6 33.9 1.0
C3D A:HAS603 4.6 34.7 1.0
O A:HIS233 4.6 37.1 1.0
CHB A:HAS603 4.6 35.2 1.0
O A:GLY232 4.8 36.0 1.0
FE A:HAS603 4.8 37.7 1.0
CHA A:HAS603 5.0 33.0 1.0

Copper binding site 2 out of 3 in 9gdf

Go back to Copper Binding Sites List in 9gdf
Copper binding site 2 out of 3 in the Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:48.7
occ:1.00
 CU1 B:CUA202 0.0 48.7 1.0
ND1 B:HIS157 2.1 35.5 1.0
O B:GLN151 2.2 44.9 1.0
SG B:CYS153 2.3 37.1 1.0
SG B:CYS149 2.4 39.2 1.0
CU2 B:CUA202 2.5 37.0 1.0
CE1 B:HIS157 3.0 38.5 1.0
CG B:HIS157 3.1 38.0 1.0
CB B:CYS153 3.3 36.8 1.0
C B:GLN151 3.3 34.8 1.0
CB B:CYS149 3.4 39.5 1.0
N B:CYS153 3.5 34.5 1.0
CB B:HIS157 3.6 34.0 1.0
CA B:HIS157 3.8 37.0 1.0
CA B:CYS153 4.0 38.3 1.0
C B:TYR152 4.1 34.8 1.0
NE2 B:HIS157 4.1 37.0 1.0
CA B:TYR152 4.1 37.3 1.0
N B:TYR152 4.1 37.0 1.0
O B:CYS149 4.2 37.9 1.0
CD2 B:HIS157 4.2 36.8 1.0
N B:GLN151 4.2 39.1 1.0
ND1 B:HIS114 4.3 33.4 1.0
O B:HIS157 4.3 34.3 1.0
C B:CYS149 4.3 37.8 1.0
CA B:GLN151 4.4 39.6 1.0
SD B:MET160 4.5 38.5 1.0
CA B:CYS149 4.5 39.9 1.0
C B:HIS157 4.5 38.8 1.0
CB B:MET160 4.9 35.5 1.0
N B:ASN150 4.9 34.1 1.0
N B:HIS157 5.0 36.4 1.0

Copper binding site 3 out of 3 in 9gdf

Go back to Copper Binding Sites List in 9gdf
Copper binding site 3 out of 3 in the Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Chloride Bound Structure of Oxidized BA3-Type Cytochrome C Oxidase Confirmed By Single-Wavelength Anomalous Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:37.0
occ:1.00
 CU2 B:CUA202 0.0 37.0 1.0
ND1 B:HIS114 2.1 33.4 1.0
SG B:CYS149 2.3 39.2 1.0
SG B:CYS153 2.4 37.1 1.0
SD B:MET160 2.4 38.5 1.0
CU1 B:CUA202 2.5 48.7 1.0
CE1 B:HIS114 2.9 36.7 1.0
CG B:HIS114 3.2 36.0 1.0
CB B:CYS153 3.2 36.8 1.0
CE B:MET160 3.2 37.2 1.0
CB B:CYS149 3.3 39.5 1.0
CB B:HIS114 3.6 37.9 1.0
CG B:MET160 3.7 35.3 1.0
O B:GLN151 4.0 44.9 1.0
NE2 B:HIS114 4.1 38.2 1.0
CA B:HIS114 4.1 39.1 1.0
CB B:MET160 4.1 35.5 1.0
CD2 B:HIS114 4.2 35.2 1.0
ND1 B:HIS157 4.5 35.5 1.0
CA B:CYS153 4.6 38.3 1.0
CA B:CYS149 4.8 39.9 1.0
O B:ILE113 4.8 37.2 1.0
CD1 B:PHE88 4.8 32.5 1.0
N B:GLY115 4.8 38.1 1.0
N B:CYS153 4.9 34.5 1.0
O B:PHE86 5.0 32.5 1.0

Reference:

D.Zoric, J.Johannesson, A.Kabbinale, E.Sandelin, A.Vallejos, S.Ghosh, P.Dahl, J.Ronnholm, M.Bjelcic, A.Finke, C.Bostedt, C.Bacellar Cases Da Silveira, E.Beale, C.Cirelli, P.Johnson, D.Ozerov, S.Boutet, A.Batyuk, C.Kupitz, A.Peck, F.Poitevin, R.Sierra, S.Lisova, C.Wallentin, G.Branden, L.Ostojic, J.Glerup, R.Neutze. Structural Changes in Cytochrome C Oxidase Following the Reduction of Dioxygen to Water To Be Published.
Page generated: Sat Aug 23 01:06:05 2025

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