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Copper in PDB 5zcq: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days

Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days

All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days:
1.9.3.1;

Protein crystallography data

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days, PDB code: 5zcq was solved by A.Shimada, K.Hatano, H.Tadehara, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.330, 204.832, 177.691, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.2

Other elements in 5zcq:

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 6 atoms
Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days (pdb code 5zcq). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days, PDB code: 5zcq:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5zcq

Go back to Copper Binding Sites List in 5zcq
Copper binding site 1 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:23.6
occ:1.00
N1 A:AZI607 1.4 17.4 0.5
NE2 A:HIS291 2.0 21.1 1.0
ND1 A:HIS240 2.0 19.4 1.0
NE2 A:HIS290 2.0 22.1 1.0
N2 A:AZI607 2.5 24.2 0.5
N2 A:AZI607 2.5 26.1 0.5
N3 A:AZI607 2.5 20.1 0.5
CE1 A:HIS291 2.9 20.3 1.0
CD2 A:HIS291 2.9 20.6 1.0
CE1 A:HIS290 3.0 22.6 1.0
N1 A:AZI607 3.0 21.3 0.5
CE1 A:HIS240 3.0 21.8 1.0
CG A:HIS240 3.0 19.8 1.0
CD2 A:HIS290 3.1 22.3 1.0
N3 A:AZI606 3.2 20.7 0.5
CB A:HIS240 3.3 20.1 1.0
N2 A:AZI606 3.4 21.5 0.5
N3 A:AZI607 3.8 16.3 0.5
CA A:HIS240 3.8 19.5 1.0
ND1 A:HIS291 4.0 20.2 1.0
N1 A:AZI606 4.1 20.7 0.5
CG A:HIS291 4.1 20.0 1.0
ND1 A:HIS290 4.1 22.6 1.0
NE2 A:HIS240 4.1 19.5 1.0
CD2 A:HIS240 4.2 20.9 1.0
CG A:HIS290 4.2 22.1 1.0
C1A A:HEA602 4.5 19.4 0.5
NA A:HEA602 4.6 20.4 0.5
N A:HIS240 4.7 19.2 1.0
ND A:HEA602 4.7 18.4 0.5
C4D A:HEA602 4.7 18.5 0.5
C1A A:HEA602 4.7 20.7 0.5
CHA A:HEA602 4.7 20.6 0.5
CG2 A:VAL243 4.8 20.7 1.0
C4A A:HEA602 4.8 20.1 0.5
C2A A:HEA602 4.8 19.3 0.5
CHA A:HEA602 4.8 20.3 0.5
NA A:HEA602 4.9 21.9 0.5
C A:HIS240 4.9 18.4 1.0
FE A:HEA602 5.0 20.3 0.5
FE A:HEA602 5.0 21.2 0.5

Copper binding site 2 out of 6 in 5zcq

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Copper binding site 2 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:23.9
occ:1.00
CU1 B:CUA302 0.0 23.9 1.0
ND1 B:HIS161 2.0 22.6 1.0
SG B:CYS196 2.3 22.9 1.0
SG B:CYS200 2.3 22.5 1.0
SD B:MET207 2.4 24.1 1.0
CU2 B:CUA302 2.5 23.5 1.0
CE1 B:HIS161 3.0 22.3 1.0
CE B:MET207 3.1 22.7 1.0
CG B:HIS161 3.2 22.4 1.0
CB B:CYS200 3.3 21.3 1.0
CB B:CYS196 3.4 23.1 1.0
CG B:MET207 3.5 23.3 1.0
CB B:HIS161 3.6 20.9 1.0
O B:GLU198 4.0 23.7 1.0
NE2 B:HIS161 4.2 22.3 1.0
CA B:HIS161 4.2 20.8 1.0
CD2 B:HIS161 4.3 21.7 1.0
ND1 B:HIS204 4.4 22.2 1.0
CA B:HIS204 4.7 23.1 1.0
CA B:CYS200 4.7 22.6 1.0
O B:HIS102 4.7 24.2 1.0
O B:LEU160 4.7 22.9 1.0
CD1 B:TRP104 4.7 23.3 1.0
CA B:CYS196 4.7 21.7 1.0
O B:HIS204 4.9 24.2 1.0
CB B:MET207 4.9 24.0 1.0

Copper binding site 3 out of 6 in 5zcq

Go back to Copper Binding Sites List in 5zcq
Copper binding site 3 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:23.5
occ:1.00
CU2 B:CUA302 0.0 23.5 1.0
ND1 B:HIS204 2.0 22.2 1.0
SG B:CYS200 2.3 22.5 1.0
SG B:CYS196 2.3 22.9 1.0
O B:GLU198 2.4 23.7 1.0
CU1 B:CUA302 2.5 23.9 1.0
CE1 B:HIS204 2.9 21.7 1.0
CG B:HIS204 3.1 22.8 1.0
CB B:CYS196 3.3 23.1 1.0
CB B:CYS200 3.3 21.3 1.0
C B:GLU198 3.5 20.7 1.0
CB B:HIS204 3.5 20.9 1.0
CA B:HIS204 3.6 23.1 1.0
N B:CYS200 3.7 21.9 1.0
O B:HIS204 3.8 24.2 1.0
NE2 B:HIS204 4.1 22.0 1.0
N B:GLU198 4.1 21.5 1.0
ND1 B:HIS161 4.1 22.6 1.0
CD2 B:HIS204 4.1 23.9 1.0
C B:HIS204 4.1 22.6 1.0
CA B:CYS200 4.1 22.6 1.0
C B:ILE199 4.2 22.0 1.0
C B:CYS196 4.2 21.4 1.0
O B:CYS196 4.2 22.3 1.0
CA B:ILE199 4.2 22.7 1.0
N B:ILE199 4.3 21.6 1.0
SD B:MET207 4.3 24.1 1.0
CA B:CYS196 4.4 21.7 1.0
CA B:GLU198 4.5 22.4 1.0
CG B:MET207 4.6 23.3 1.0
N B:SER197 4.7 21.7 1.0
N B:HIS204 4.8 24.1 1.0
CA B:HIS161 4.9 20.8 1.0

Copper binding site 4 out of 6 in 5zcq

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Copper binding site 4 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:26.3
occ:1.00
N1 N:AZI607 1.4 20.1 0.5
NE2 N:HIS291 2.0 25.2 1.0
NE2 N:HIS290 2.0 24.9 1.0
ND1 N:HIS240 2.0 22.3 1.0
N2 N:AZI607 2.5 28.0 0.5
N3 N:AZI607 2.6 25.3 0.5
N2 N:AZI607 2.6 29.9 0.5
CE1 N:HIS291 2.9 23.9 1.0
CD2 N:HIS291 3.0 25.4 1.0
CE1 N:HIS290 3.0 23.1 1.0
CG N:HIS240 3.0 23.5 1.0
CE1 N:HIS240 3.0 21.8 1.0
CD2 N:HIS290 3.1 24.6 1.0
N3 N:AZI606 3.2 24.0 0.5
N1 N:AZI607 3.2 26.2 0.5
CB N:HIS240 3.3 22.2 1.0
N2 N:AZI606 3.4 23.0 0.5
N3 N:AZI607 3.8 19.6 0.5
CA N:HIS240 3.8 22.1 1.0
ND1 N:HIS291 4.0 23.6 1.0
CG N:HIS291 4.1 23.4 1.0
N1 N:AZI606 4.1 21.0 0.5
ND1 N:HIS290 4.1 24.8 1.0
NE2 N:HIS240 4.1 21.0 1.0
CD2 N:HIS240 4.1 22.4 1.0
CG N:HIS290 4.2 24.1 1.0
C1A N:HEA602 4.5 22.6 0.5
NA N:HEA602 4.6 23.8 0.5
N N:HIS240 4.7 21.4 1.0
C4D N:HEA602 4.7 24.7 0.5
ND N:HEA602 4.7 24.0 0.5
C4A N:HEA602 4.8 22.7 0.5
C1A N:HEA602 4.8 26.9 0.5
CHA N:HEA602 4.8 24.2 0.5
CG2 N:VAL243 4.9 22.7 1.0
CHA N:HEA602 4.9 23.5 0.5
C2A N:HEA602 4.9 23.7 0.5
NA N:HEA602 4.9 26.4 0.5
FE N:HEA602 5.0 23.2 0.5
FE N:HEA602 5.0 24.6 0.5
C N:HIS240 5.0 22.8 1.0
C3A N:HEA602 5.0 23.5 0.5

Copper binding site 5 out of 6 in 5zcq

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Copper binding site 5 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:30.0
occ:1.00
CU1 O:CUA301 0.0 30.0 1.0
ND1 O:HIS161 2.0 29.3 1.0
SG O:CYS196 2.3 29.6 1.0
SG O:CYS200 2.3 29.1 1.0
SD O:MET207 2.4 31.2 1.0
CU2 O:CUA301 2.5 30.1 1.0
CE1 O:HIS161 3.0 28.4 1.0
CE O:MET207 3.1 29.8 1.0
CG O:HIS161 3.1 25.7 1.0
CB O:CYS200 3.3 28.3 1.0
CB O:CYS196 3.3 29.9 1.0
CG O:MET207 3.5 28.9 1.0
CB O:HIS161 3.6 26.6 1.0
O O:GLU198 4.0 29.0 1.0
NE2 O:HIS161 4.1 29.1 1.0
CA O:HIS161 4.2 27.2 1.0
CD2 O:HIS161 4.2 28.5 1.0
ND1 O:HIS204 4.4 28.4 1.0
CA O:HIS204 4.6 28.9 1.0
CD1 O:TRP104 4.7 31.1 1.0
O O:HIS102 4.7 31.3 1.0
O O:LEU160 4.7 28.7 1.0
CA O:CYS200 4.7 29.4 1.0
CA O:CYS196 4.7 28.1 1.0
O O:HIS204 4.9 30.3 1.0
CB O:MET207 4.9 30.3 1.0

Copper binding site 6 out of 6 in 5zcq

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Copper binding site 6 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 10 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:30.1
occ:1.00
CU2 O:CUA301 0.0 30.1 1.0
ND1 O:HIS204 2.0 28.4 1.0
SG O:CYS200 2.3 29.1 1.0
SG O:CYS196 2.3 29.6 1.0
O O:GLU198 2.4 29.0 1.0
CU1 O:CUA301 2.5 30.0 1.0
CE1 O:HIS204 3.0 27.8 1.0
CG O:HIS204 3.1 27.6 1.0
CB O:CYS196 3.3 29.9 1.0
CB O:CYS200 3.4 28.3 1.0
C O:GLU198 3.5 26.7 1.0
CB O:HIS204 3.5 28.6 1.0
CA O:HIS204 3.6 28.9 1.0
N O:CYS200 3.7 29.2 1.0
O O:HIS204 3.8 30.3 1.0
NE2 O:HIS204 4.1 27.7 1.0
N O:GLU198 4.1 27.9 1.0
C O:HIS204 4.1 29.1 1.0
CD2 O:HIS204 4.1 27.4 1.0
ND1 O:HIS161 4.2 29.3 1.0
C O:ILE199 4.2 27.4 1.0
CA O:CYS200 4.2 29.4 1.0
O O:CYS196 4.2 29.3 1.0
CA O:ILE199 4.2 26.5 1.0
C O:CYS196 4.2 29.3 1.0
N O:ILE199 4.3 24.9 1.0
SD O:MET207 4.3 31.2 1.0
CA O:CYS196 4.4 28.1 1.0
CA O:GLU198 4.5 27.5 1.0
N O:SER197 4.6 28.9 1.0
CG O:MET207 4.7 28.9 1.0
N O:HIS204 4.8 30.3 1.0
CA O:HIS161 4.9 27.2 1.0

Reference:

A.Shimada, K.Hatano, H.Tadehara, N.Yano, K.Shinzawa-Itoh, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. X-Ray Structural Analyses of Azide-Bound Cytochromecoxidases Reveal That the H-Pathway Is Critically Important For the Proton-Pumping Activity. J. Biol. Chem. V. 293 14868 2018.
ISSN: ESSN 1083-351X
PubMed: 30077971
DOI: 10.1074/JBC.RA118.003123
Page generated: Mon Jul 14 05:44:32 2025

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