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Copper in PDB 5z85: The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days

Enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days

All present enzymatic activity of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days:
1.9.3.1;

Protein crystallography data

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5z85 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 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.126, 205.893, 177.576, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.9

Other elements in 5z85:

The structure of The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days (pdb code 5z85). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5z85:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5z85

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Copper binding site 1 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:25.2
occ:1.00
N1 A:AZI606 1.8 28.2 1.0
NE2 A:HIS291 2.0 22.7 1.0
ND1 A:HIS240 2.0 21.9 1.0
NE2 A:HIS290 2.1 25.3 1.0
N2 A:AZI606 2.6 29.0 1.0
CE1 A:HIS291 2.9 20.1 1.0
N1 A:AZI607 3.0 34.2 1.0
CE1 A:HIS290 3.0 23.3 1.0
CD2 A:HIS291 3.0 21.9 1.0
CE1 A:HIS240 3.0 21.7 1.0
CG A:HIS240 3.0 21.1 1.0
CD2 A:HIS290 3.1 22.3 1.0
N2 A:AZI607 3.2 31.0 1.0
CB A:HIS240 3.3 20.3 1.0
N3 A:AZI606 3.8 28.9 1.0
CA A:HIS240 3.9 19.8 1.0
N3 A:AZI607 3.9 31.6 1.0
ND1 A:HIS291 4.0 21.8 1.0
CG A:HIS291 4.1 22.2 1.0
ND1 A:HIS290 4.1 22.3 1.0
NE2 A:HIS240 4.2 20.4 1.0
CD2 A:HIS240 4.2 21.3 1.0
CG A:HIS290 4.2 23.3 1.0
C1A A:HEA602 4.5 21.1 0.5
NA A:HEA602 4.6 21.5 0.5
ND A:HEA602 4.6 21.5 0.5
N A:HIS240 4.7 19.6 1.0
C4D A:HEA602 4.7 21.2 0.5
C1A A:HEA602 4.7 23.1 0.5
CHA A:HEA602 4.7 22.1 0.5
CHA A:HEA602 4.8 22.0 0.5
CG2 A:VAL243 4.8 20.6 1.0
NA A:HEA602 4.9 23.9 0.5
FE A:HEA602 4.9 23.5 0.5
FE A:HEA602 4.9 22.2 0.5
C4A A:HEA602 4.9 22.5 0.5
C2A A:HEA602 4.9 22.0 0.5
C4D A:HEA602 4.9 21.9 0.5
ND A:HEA602 5.0 24.5 0.5
C A:HIS240 5.0 20.2 1.0

Copper binding site 2 out of 6 in 5z85

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Copper binding site 2 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:27.0
occ:1.00
CU1 B:CUA301 0.0 27.0 1.0
ND1 B:HIS161 2.0 24.9 1.0
SG B:CYS196 2.3 25.5 1.0
SG B:CYS200 2.4 25.2 1.0
SD B:MET207 2.4 27.2 1.0
CU2 B:CUA301 2.5 26.0 1.0
CE1 B:HIS161 3.0 23.1 1.0
CE B:MET207 3.1 25.4 1.0
CG B:HIS161 3.2 24.3 1.0
CB B:CYS200 3.3 23.8 1.0
CB B:CYS196 3.4 23.2 1.0
CG B:MET207 3.5 27.5 1.0
CB B:HIS161 3.6 22.4 1.0
O B:GLU198 4.0 26.8 1.0
NE2 B:HIS161 4.2 23.9 1.0
CA B:HIS161 4.2 24.2 1.0
CD2 B:HIS161 4.3 24.4 1.0
ND1 B:HIS204 4.4 26.1 1.0
CA B:HIS204 4.7 27.9 1.0
CD1 B:TRP104 4.7 26.7 1.0
O B:HIS102 4.7 25.9 1.0
CA B:CYS200 4.7 24.9 1.0
O B:LEU160 4.7 24.4 1.0
CA B:CYS196 4.8 25.1 1.0
CB B:MET207 4.9 27.2 1.0
O B:HIS204 4.9 27.4 1.0

Copper binding site 3 out of 6 in 5z85

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Copper binding site 3 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:26.0
occ:1.00
CU2 B:CUA301 0.0 26.0 1.0
ND1 B:HIS204 2.0 26.1 1.0
SG B:CYS200 2.3 25.2 1.0
SG B:CYS196 2.3 25.5 1.0
O B:GLU198 2.3 26.8 1.0
CU1 B:CUA301 2.5 27.0 1.0
CE1 B:HIS204 2.8 26.6 1.0
CG B:HIS204 3.1 26.6 1.0
CB B:CYS196 3.3 23.2 1.0
CB B:CYS200 3.3 23.8 1.0
C B:GLU198 3.4 22.8 1.0
CB B:HIS204 3.6 25.8 1.0
CA B:HIS204 3.6 27.9 1.0
N B:CYS200 3.7 23.8 1.0
O B:HIS204 3.8 27.4 1.0
NE2 B:HIS204 4.0 24.6 1.0
N B:GLU198 4.1 23.6 1.0
ND1 B:HIS161 4.1 24.9 1.0
CD2 B:HIS204 4.1 24.1 1.0
C B:HIS204 4.1 26.6 1.0
CA B:CYS200 4.2 24.9 1.0
C B:ILE199 4.2 22.8 1.0
CA B:ILE199 4.2 24.2 1.0
N B:ILE199 4.3 23.2 1.0
O B:CYS196 4.3 24.1 1.0
C B:CYS196 4.3 26.2 1.0
SD B:MET207 4.3 27.2 1.0
CA B:CYS196 4.4 25.1 1.0
CA B:GLU198 4.5 24.2 1.0
N B:SER197 4.7 24.8 1.0
CG B:MET207 4.7 27.5 1.0
N B:HIS204 4.9 28.4 1.0
CA B:HIS161 4.9 24.2 1.0

Copper binding site 4 out of 6 in 5z85

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Copper binding site 4 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:28.8
occ:1.00
N1 N:AZI606 1.8 35.1 1.0
ND1 N:HIS240 2.0 25.8 1.0
NE2 N:HIS291 2.0 28.6 1.0
NE2 N:HIS290 2.1 27.7 1.0
N2 N:AZI606 2.7 33.5 1.0
CE1 N:HIS291 2.9 24.8 1.0
CD2 N:HIS291 3.0 26.4 1.0
CE1 N:HIS240 3.0 23.8 1.0
CG N:HIS240 3.0 25.9 1.0
CE1 N:HIS290 3.1 25.1 1.0
N1 N:AZI607 3.1 38.2 1.0
CD2 N:HIS290 3.1 25.4 1.0
CB N:HIS240 3.3 23.6 1.0
N2 N:AZI607 3.3 34.3 1.0
CA N:HIS240 3.8 23.8 1.0
N3 N:AZI606 3.9 34.0 1.0
N3 N:AZI607 4.1 32.4 1.0
ND1 N:HIS291 4.1 26.9 1.0
CG N:HIS291 4.1 26.6 1.0
NE2 N:HIS240 4.1 22.7 1.0
CD2 N:HIS240 4.2 24.5 1.0
ND1 N:HIS290 4.2 24.5 1.0
CG N:HIS290 4.3 27.2 1.0
C1A N:HEA602 4.5 25.5 0.5
ND N:HEA602 4.6 24.6 0.5
NA N:HEA602 4.6 25.7 0.5
C4D N:HEA602 4.6 25.1 0.5
N N:HIS240 4.7 22.2 1.0
CHA N:HEA602 4.8 24.8 0.5
CG2 N:VAL243 4.8 23.7 1.0
C1A N:HEA602 4.8 27.9 0.5
CHA N:HEA602 4.8 25.6 0.5
C4A N:HEA602 4.9 25.9 0.5
FE N:HEA602 4.9 26.5 0.5
FE N:HEA602 4.9 25.6 0.5
NA N:HEA602 4.9 29.4 0.5
C4D N:HEA602 4.9 27.4 0.5
C2A N:HEA602 4.9 25.8 0.5
C N:HIS240 4.9 23.0 1.0
ND N:HEA602 4.9 26.4 0.5

Copper binding site 5 out of 6 in 5z85

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Copper binding site 5 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:32.6
occ:1.00
CU1 O:CUA301 0.0 32.6 1.0
ND1 O:HIS161 2.1 32.1 1.0
SG O:CYS196 2.3 33.2 1.0
SG O:CYS200 2.3 31.4 1.0
SD O:MET207 2.4 32.2 1.0
CU2 O:CUA301 2.5 31.8 1.0
CE1 O:HIS161 2.9 30.3 1.0
CE O:MET207 3.1 28.9 1.0
CG O:HIS161 3.2 28.0 1.0
CB O:CYS200 3.3 28.6 1.0
CB O:CYS196 3.4 32.4 1.0
CG O:MET207 3.6 32.5 1.0
CB O:HIS161 3.7 29.4 1.0
O O:GLU198 3.9 30.7 1.0
NE2 O:HIS161 4.1 30.4 1.0
CA O:HIS161 4.2 29.1 1.0
CD2 O:HIS161 4.3 29.6 1.0
ND1 O:HIS204 4.4 32.6 1.0
O O:HIS102 4.7 32.9 1.0
CA O:HIS204 4.7 31.0 1.0
CA O:CYS200 4.7 31.9 1.0
CD1 O:TRP104 4.7 35.6 1.0
O O:LEU160 4.7 29.9 1.0
CA O:CYS196 4.8 31.9 1.0
CB O:MET207 4.9 32.9 1.0
O O:HIS204 4.9 32.2 1.0

Copper binding site 6 out of 6 in 5z85

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Copper binding site 6 out of 6 in the The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 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 The Structure of Azide-Bound Cytochrome C Oxidase Determined Using the Another Batch Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:31.8
occ:1.00
CU2 O:CUA301 0.0 31.8 1.0
ND1 O:HIS204 2.0 32.6 1.0
O O:GLU198 2.3 30.7 1.0
SG O:CYS200 2.3 31.4 1.0
SG O:CYS196 2.3 33.2 1.0
CU1 O:CUA301 2.5 32.6 1.0
CE1 O:HIS204 2.8 31.9 1.0
CG O:HIS204 3.1 30.3 1.0
CB O:CYS196 3.2 32.4 1.0
CB O:CYS200 3.3 28.6 1.0
C O:GLU198 3.4 27.5 1.0
CB O:HIS204 3.6 29.9 1.0
CA O:HIS204 3.6 31.0 1.0
N O:CYS200 3.7 32.0 1.0
O O:HIS204 3.8 32.2 1.0
NE2 O:HIS204 4.0 28.7 1.0
N O:GLU198 4.1 29.2 1.0
CD2 O:HIS204 4.2 28.0 1.0
C O:ILE199 4.2 31.3 1.0
CA O:CYS200 4.2 31.9 1.0
ND1 O:HIS161 4.2 32.1 1.0
C O:HIS204 4.2 31.0 1.0
CA O:ILE199 4.2 29.7 1.0
C O:CYS196 4.2 31.6 1.0
N O:ILE199 4.2 28.5 1.0
O O:CYS196 4.3 30.7 1.0
SD O:MET207 4.4 32.2 1.0
CA O:CYS196 4.4 31.9 1.0
CA O:GLU198 4.4 31.1 1.0
N O:SER197 4.6 31.9 1.0
CG O:MET207 4.7 32.5 1.0
N O:HIS204 4.9 31.7 1.0
CA O:HIS161 4.9 29.1 1.0
CE1 O:HIS161 5.0 30.3 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: Sun Dec 13 11:20:55 2020

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